CAPN3 (calpain 3)

Gene

• Entrez ID: 825
• Gene name: Calpain 3
• Gene symbol: CAPN3
• Synonyms (NCBI Gene): CANP3, CANPL3, LGMD2, LGMD2A, LGMDD4, LGMDR1, nCL-1, p94
• Chromosome: 15
• Chromosome location: 15q15.1
• Summary: Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically bind

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28364528	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant, synonymous variant, coding sequence variant
rs79440238	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, 5 prime UTR variant
rs80338801	G>A	Pathogenic	Genic upstream transcript variant, splice acceptor variant
rs80338802	G>A,C	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs80338803	AAA>-,AA,AAAA	Uncertain-significance, pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, intron variant, inframe deletion
rs80338804	->TC	Pathogenic	Coding sequence variant, frameshift variant
rs111806046	A>C,G	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, synonymous variant
rs121434544	G>A,C,T	Uncertain-significance, pathogenic	Upstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs121434546	C>T	Pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant
rs121434547	C>T	Uncertain-significance, pathogenic-likely-pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant
rs121434548	G>A,C	Pathogenic	Upstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs138867099	C>A,T	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant
rs139836397	T>G	Likely-pathogenic, uncertain-significance	Missense variant, genic upstream transcript variant, coding sequence variant
rs141656719	C>T	Pathogenic-likely-pathogenic, pathogenic	Upstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs142004418	C>G,T	Uncertain-significance, pathogenic	Upstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs143139259	A>G,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs146069933	C>T	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, synonymous variant
rs146309264	G>A	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs146403258	G>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, missense variant
rs146923842	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs147764579	G>A	Likely-pathogenic, pathogenic	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs147774793	C>A,G,T	Conflicting-interpretations-of-pathogenicity, pathogenic, benign-likely-benign	Synonymous variant, stop gained, coding sequence variant
rs147914333	C>T	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, synonymous variant
rs148044781	T>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs149095128	C>A	Pathogenic-likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs149914792	G>A,C	Pathogenic-likely-pathogenic, uncertain-significance	Genic upstream transcript variant, coding sequence variant, missense variant
rs150226817	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs187279903	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs199806879	C>T	Likely-pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, missense variant, intron variant
rs199884116	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, synonymous variant
rs199978708	C>G	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, intron variant, genic upstream transcript variant
rs200379491	A>G	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs200583904	C>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs200646556	C>T	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs201294691	C>A,G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs201607149	G>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant, intron variant
rs201736037	A>G	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, missense variant
rs201892814	C>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, pathogenic	Upstream transcript variant, intron variant, genic upstream transcript variant
rs202019404	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, intron variant, synonymous variant
rs267606703	G>C	Pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs368385372	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, synonymous variant
rs369552114	G>A	Likely-pathogenic, pathogenic	Splice acceptor variant
rs369784333	G>A	Likely-pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs370231427	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, synonymous variant
rs370313391	C>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, genic upstream transcript variant, synonymous variant
rs371577901	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs372401631	G>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, synonymous variant
rs372438001	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, missense variant
rs372450879	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic upstream transcript variant, synonymous variant
rs374665929	A>C,G	Pathogenic	Intron variant, genic upstream transcript variant
rs376107921	G>A,C	Pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs398123143	G>A	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, missense variant
rs398123146	->T	Likely-pathogenic, pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs398123147	->GTCA	Pathogenic	Coding sequence variant, frameshift variant
rs398123150	->GTTGATTGCA	Pathogenic	Coding sequence variant, intron variant, genic upstream transcript variant, frameshift variant
rs528417986	C>A,T	Likely-pathogenic, pathogenic	Genic upstream transcript variant, missense variant, intron variant, synonymous variant, coding sequence variant
rs530529988	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, missense variant, synonymous variant, coding sequence variant
rs557164942	C>G,T	Likely-pathogenic, pathogenic-likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant, genic upstream transcript variant, upstream transcript variant
rs587780289	CA>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant
rs587780290	G>A	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs727503839	G>T	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, upstream transcript variant
rs746075428	GGA>-	Likely-pathogenic	Inframe deletion, genic upstream transcript variant, coding sequence variant, upstream transcript variant
rs747557404	G>C	Pathogenic	Genic upstream transcript variant, upstream transcript variant, splice acceptor variant
rs749099493	C>T	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs749863676	A>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic upstream transcript variant, coding sequence variant, missense variant
rs750083132	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs750443041	G>T	Pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant
rs752848213	C>G,T	Pathogenic, likely-benign	Stop gained, coding sequence variant, upstream transcript variant, genic upstream transcript variant, synonymous variant
rs753360208	->T	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant
rs753686702	C>T	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, synonymous variant
rs754761503	G>-	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant, upstream transcript variant
rs758058910	C>A,T	Pathogenic	Missense variant, synonymous variant, genic upstream transcript variant, coding sequence variant
rs760196248	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant, genic upstream transcript variant
rs760205277	G>-	Pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs760626912	T>G	Pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant
rs760919949	->GT	Likely-pathogenic	Splice donor variant, coding sequence variant
rs761211705	G>A,C	Pathogenic	Intron variant, genic upstream transcript variant
rs761257703	GGG>-,GGGG	Pathogenic	Intron variant, frameshift variant, inframe deletion, genic upstream transcript variant, coding sequence variant
rs761757153	C>G	Likely-pathogenic	Intron variant
rs761897806	->TC	Pathogenic	Frameshift variant, coding sequence variant
rs761935462	T>G	Likely-pathogenic	Splice donor variant
rs762471207	A>-	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant
rs763649825	CTCT>-,CT	Pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs764086484	GACA>-	Pathogenic	Frameshift variant, coding sequence variant
rs764459544	A>G	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs766156798	GACA>-	Pathogenic, likely-pathogenic	Intron variant, splice acceptor variant, genic upstream transcript variant, coding sequence variant
rs766334893	G>T	Pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant
rs766917640	G>A	Likely-pathogenic	Splice donor variant
rs767739787	G>A	Pathogenic-likely-pathogenic	Missense variant, genic upstream transcript variant, upstream transcript variant, coding sequence variant
rs768090444	C>G,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs768374736	G>A,C,T	Pathogenic	Splice donor variant
rs769688710	A>G	Likely-pathogenic	Splice acceptor variant
rs770894443	G>A,T	Uncertain-significance, pathogenic-likely-pathogenic	Missense variant, synonymous variant, coding sequence variant
rs773001194	G>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs773827877	G>A,C	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs774048743	G>A	Pathogenic, pathogenic-likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs774273767	C>G,T	Uncertain-significance, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs775130589	->A	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs775217052	T>A	Pathogenic	Splice donor variant
rs775453643	T>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, missense variant
rs776043976	C>G,T	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs776059672	T>-,TT	Pathogenic, likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant, stop gained
rs777323132	C>T	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs777483913	C>T	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs777636094	G>A,T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, stop gained, missense variant
rs778768583	G>C	Pathogenic	Coding sequence variant, missense variant
rs780680647	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs780810538	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs781013226	G>-	Pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs786205491	G>A	Likely-pathogenic	Splice acceptor variant
rs794726871	C>T	Pathogenic-likely-pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs794727318	C>G,T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs794727697	GAA>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, inframe deletion
rs863224956	G>A,T	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs863224957	C>T	Pathogenic	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs863224958	G>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs863224959	C>G,T	Pathogenic, uncertain-significance	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs863224960	G>A,T	Pathogenic	5 prime UTR variant, coding sequence variant, stop gained, missense variant
rs863224961	G>C,T	Pathogenic	Splice donor variant
rs863224962	A>G	Pathogenic-likely-pathogenic	Splice acceptor variant
rs863224965	TCCTACGAAGCTCTGAAAGGT>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, inframe deletion
rs863224966	GATA>CTT	Pathogenic	Intron variant, frameshift variant, genic upstream transcript variant, coding sequence variant
rs867628179	C>A,T	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs868791726	C>A,T	Likely-pathogenic	Synonymous variant, coding sequence variant, missense variant
rs869312852	CATTGA>-	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, inframe deletion
rs886039597	G>C	Uncertain-significance, likely-pathogenic	Intron variant, genic upstream transcript variant
rs886041335	A>G	Pathogenic, likely-pathogenic	Splice acceptor variant
rs886042108	G>C,T	Pathogenic, likely-pathogenic	Splice acceptor variant
rs886042418	CA>-	Pathogenic	Frameshift variant, coding sequence variant
rs886042439	C>A	Pathogenic	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, stop gained
rs886042478	C>T	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs886042557	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs886042573	TG>-	Pathogenic, likely-pathogenic	Frameshift variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant
rs886042895	A>G	Uncertain-significance, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs886042903	G>C	Likely-pathogenic	Intron variant, upstream transcript variant, genic upstream transcript variant
rs886042927	C>T	Pathogenic	5 prime UTR variant, coding sequence variant, stop gained
rs886042964	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs886043222	->T	Pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs886043333	ACG>-	Uncertain-significance, likely-pathogenic	Coding sequence variant, inframe deletion
rs886043432	G>A	Likely-pathogenic	Synonymous variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant
rs886043705	C>-	Pathogenic	Frameshift variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant
rs886043752	G>A	Pathogenic, likely-pathogenic	Intron variant, splice acceptor variant
rs886044004	->G	Pathogenic	Frameshift variant, coding sequence variant, initiator codon variant
rs886044052	G>A,C	Pathogenic, uncertain-significance	Splice acceptor variant
rs886044417	->A	Pathogenic	Intron variant, frameshift variant, coding sequence variant
rs886044475	G>A	Pathogenic	Splice donor variant
rs886044527	G>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs988027905	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, genic upstream transcript variant
rs1057524468	T>A,C	Pathogenic, likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1064793620	AT>-	Pathogenic, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs1085307534	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1085307995	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs1274808359	C>T	Pathogenic-likely-pathogenic, pathogenic	Upstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs1275289254	G>A,T	Pathogenic	Splice donor variant, upstream transcript variant, genic upstream transcript variant
rs1293496023	TG>-	Pathogenic-likely-pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1334369407	C>-	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, upstream transcript variant, coding sequence variant
rs1345121557	G>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs1366387924	C>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant
rs1447774727	->T	Likely-pathogenic	Stop gained, coding sequence variant
rs1459288402	G>A	Pathogenic	Genic upstream transcript variant, splice donor variant
rs1555417257	T>C	Likely-pathogenic	Missense variant, initiator codon variant, genic upstream transcript variant
rs1555417271	C>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555417321	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555420634	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs1555420639	->G	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555420642	GATG>AT	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555420647	CATGTACAAGA>-	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555420765	T>C	Likely-pathogenic	Intron variant, missense variant, coding sequence variant, genic upstream transcript variant
rs1555421263	G>A	Likely-pathogenic	Splice acceptor variant, genic upstream transcript variant
rs1555421271	T>G	Likely-pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs1555421280	G>A	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1555421293	G>A	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1555421523	G>A	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1555421524	G>A	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1555421842	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555421847	G>T	Likely-pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs1555421854	CT>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555421856	->T	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555421871	G>-	Pathogenic	Frameshift variant, coding sequence variant, genic upstream transcript variant
rs1555422136	T>C	Uncertain-significance, likely-pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant
rs1555422145	T>C	Pathogenic	Splice donor variant, genic upstream transcript variant, upstream transcript variant
rs1555422293	C>-	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant
rs1555422298	->CACC	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant
rs1555422832	A>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1555422839	G>T	Likely-pathogenic	Intron variant, stop gained, coding sequence variant
rs1555422847	A>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1555422851	GGTGTCTGGGCATGTGGCA>-	Likely-pathogenic	Splice donor variant, coding sequence variant, intron variant
rs1555422856	T>C	Likely-pathogenic	Splice donor variant, intron variant
rs1555422954	TG>-	Likely-pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant
rs1555423015	T>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1555423021	->AAACA	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555423027	G>-	Likely-pathogenic	Splice donor variant
rs1555423046	AC>-	Pathogenic	Coding sequence variant, frameshift variant
rs1555423060	T>C	Pathogenic	Splice donor variant
rs1555423146	T>C	Likely-pathogenic	Splice donor variant
rs1555423217	AG>TCATCT	Pathogenic	Coding sequence variant, frameshift variant
rs1555423219	G>TCT	Pathogenic	Coding sequence variant, frameshift variant
rs1555423222	G>T	Likely-pathogenic	Splice donor variant
rs1566983844	C>T	Pathogenic	Coding sequence variant, stop gained, intron variant
rs1566984441	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs1595794433	->T	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1595826673	A>G	Pathogenic	Splice acceptor variant, genic upstream transcript variant
rs1595828589	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1595828703	G>A	Pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant
rs1595837172	A>-	Likely-pathogenic	Coding sequence variant, upstream transcript variant, frameshift variant, genic upstream transcript variant
rs1595838545	C>-	Pathogenic	Coding sequence variant, upstream transcript variant, frameshift variant, genic upstream transcript variant
rs1595844413	C>T	Likely-pathogenic	Coding sequence variant, stop gained, intron variant
rs1595845459	G>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs1595846922	AGAT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1595847257	C>T	Likely-pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT441014	hsa-miR-544a	HITS-CLIP	24374217
MIRT441014	hsa-miR-544a	HITS-CLIP	24374217

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IDA	9642272
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	IBA
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	IEA
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	ISS
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	TAS	9642272
GO:0005509	Function	Calcium ion binding	IEA
GO:0005509	Function	Calcium ion binding	ISS
GO:0005515	Function	Protein binding	IPI	20860623, 23357851, 23414517, 23707407, 25416956, 26871637, 27657329, 31515488, 32296183, 32814053
GO:0005634	Component	Nucleus	IDA	19386580
GO:0005634	Component	Nucleus	IEA
GO:0005730	Component	Nucleolus	IDA	27657329
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	19386580, 19556129
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0006508	Process	Proteolysis	IBA
GO:0006508	Process	Proteolysis	IDA	9642272, 18310072, 19386580, 20694146
GO:0006508	Process	Proteolysis	IEA
GO:0006508	Process	Proteolysis	IEA
GO:0006915	Process	Apoptotic process	TAS	19386580
GO:0007517	Process	Muscle organ development	TAS	7720071, 9642272
GO:0008233	Function	Peptidase activity	IDA	9642272, 23707407
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	TAS	2555341
GO:0008307	Function	Structural constituent of muscle	IEA
GO:0008307	Function	Structural constituent of muscle	ISS
GO:0012501	Process	Programmed cell death	IEA
GO:0014718	Process	Positive regulation of satellite cell activation involved in skeletal muscle regeneration	IEA
GO:0014718	Process	Positive regulation of satellite cell activation involved in skeletal muscle regeneration	ISS
GO:0014850	Process	Response to muscle activity	ISS
GO:0016787	Function	Hydrolase activity	IEA
GO:0030016	Component	Myofibril	ISS
GO:0030018	Component	Z disc	ISS
GO:0030163	Process	Protein catabolic process	IDA	27657329
GO:0030163	Process	Protein catabolic process	IMP	23357851
GO:0030239	Process	Myofibril assembly	IEA
GO:0030239	Process	Myofibril assembly	ISS
GO:0030239	Process	Myofibril assembly	TAS	9642272
GO:0030315	Component	T-tubule	ISS
GO:0031402	Function	Sodium ion binding	IEA
GO:0031402	Function	Sodium ion binding	ISS
GO:0031432	Function	Titin binding	IPI	9642272, 18310072
GO:0031648	Process	Protein destabilization	IMP	23357851
GO:0032991	Component	Protein-containing complex	IEA
GO:0032991	Component	Protein-containing complex	ISS
GO:0033234	Process	Negative regulation of protein sumoylation	IDA	20694146
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0043066	Process	Negative regulation of apoptotic process	IBA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IMP	18073330
GO:0043122	Process	Regulation of canonical NF-kappaB signal transduction	IEA
GO:0043122	Process	Regulation of canonical NF-kappaB signal transduction	IMP	18073330
GO:0045214	Process	Sarcomere organization	IEA
GO:0045214	Process	Sarcomere organization	ISS
GO:0045661	Process	Regulation of myoblast differentiation	IEA
GO:0045862	Process	Positive regulation of proteolysis	IEA
GO:0045862	Process	Positive regulation of proteolysis	ISS
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IMP	18073330
GO:0046716	Process	Muscle cell cellular homeostasis	TAS	19386580
GO:0046872	Function	Metal ion binding	IEA
GO:0051281	Process	Positive regulation of release of sequestered calcium ion into cytosol	IEA
GO:0051281	Process	Positive regulation of release of sequestered calcium ion into cytosol	ISS
GO:0051592	Process	Response to calcium ion	ISS
GO:0055103	Function	Ligase regulator activity	IDA	20694146
GO:0060090	Function	Molecular adaptor activity	IEA
GO:0060090	Function	Molecular adaptor activity	ISS
GO:0061061	Process	Muscle structure development	IEA
GO:0061061	Process	Muscle structure development	ISS
GO:0065003	Process	Protein-containing complex assembly	IEA
GO:0065003	Process	Protein-containing complex assembly	ISS
GO:0070315	Process	G1 to G0 transition involved in cell differentiation	IEA
GO:0071277	Process	Cellular response to calcium ion	IEA
GO:0071277	Process	Cellular response to calcium ion	ISS
GO:0071472	Process	Cellular response to salt stress	IEA
GO:0071472	Process	Cellular response to salt stress	ISS
GO:0072657	Process	Protein localization to membrane	IEA
GO:0072657	Process	Protein localization to membrane	ISS
GO:0097264	Process	Self proteolysis	IDA	9642272
GO:1990092	Process	Calcium-dependent self proteolysis	IDA	12482600

Other IDs

• MIM: 114240
• HGNC: 1480
• e!Ensembl: ENSG00000092529

Protein

• UniProt ID: P20807
• Protein name: Calpain-3 (EC 3.4.22.54) (Calcium-activated neutral proteinase 3) (CANP 3) (Calpain L3) (Calpain p94) (Muscle-specific calcium-activated neutral protease 3) (New calpain 1) (nCL-1)
• Protein function: Calcium-regulated non-lysosomal thiol-protease. Proteolytically cleaves CTBP1 at 'His-409'. Mediates, with UTP25, the proteasome-independent degradation of p53/TP53 (PubMed:23357851, PubMed:27657329). {ECO:0000269|PubMed:23357851, ECO:0000269|Pu
• PDB: 4OKH, 6BDT, 6BGP, 6BJD, 6BKJ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00648	Peptidase_C2	75 → 415	Calpain family cysteine protease	Family
  PF01067	Calpain_III	436 → 574	Calpain large subunit, domain III	Domain
  PF16648	Calpain_u2	583 → 653		Disordered

• Tissue specificity: TISSUE SPECIFICITY: Isoform I is skeletal muscle specific.
• Sequence:

  MPTVISASVAPRTAAEPRSPGPVPHPAQSKATEAGGGNPSGIYSAIISRNFPIIGVKEKT
  FEQLHKKCLEKKVLYVDPEFPPDETSLFYSQKFPIQFVWKRPPEICENPRFIIDGANRTD
  ICQGELGDCWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDD
  CLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFE
  IRDAPSDMYKIMKKAIERGSLMGCSIDDGTNMTYGTSPSGLNMGELIARMVRNMDNSLLQ
  DSDLDPRGSDERPTRTIIPVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPW
  GQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHFTKLEICNLTADA
  LQSDKLQTWTVSVNEGRWVRGCSAGGCRNFPDTFWTNPQYRLKLLEEDDDPDDSEVICSF
  LVALMQKNRRKDRKLGASLFTIGFAIYEVPKEMHGNKQHLQKDFFLYNASKARSKTYINM
  REVSQRFRLPPSEYVIVPSTYEPHQEGEFILRVFSEKRNLSEEVENTISVDRPVKKKKTK
  PIIFVSDRANSNKELGVDQESEEGKGKTSPDKQKQSPQPQPGSSDQESEEQQQFRNIFKQ
  IAGDDMEICADELKKVLNTVVNKHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHL
  WNKIKAWQKIFKHYDTDQSGTINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFD
  SFICCFVRLEGMFRAFHAFDKDGDGIIKLNVLEWLQLTMYA

• Sequence length: 821

Pathways

KEGG:

Cytoskeleton in muscle cells

Reactome:

Degradation of the extracellular matrix

<

Associated diseases

Causal
Disease merge term	Disease name	dbSNP ID	References
Limb-Girdle Muscular Dystrophy	muscular dystrophy, limb-girdle, autosomal dominant 4	rs760919949, rs863224964, rs767739787, rs1447774727, rs147774793, rs369552114, rs1275289254, rs1595844413, rs727503839, rs766334893, rs762471207, rs1566983844, rs201736037, rs764459544, rs863224957, rs1409503203, rs749099493, rs1459288402, rs750083132, rs764086484, rs121434547, rs863224965, rs141656719, rs886044052, rs777323132, rs761211705, rs1555420642, rs1555423222, rs1555423060, rs794727318, rs781013226, rs886042478, rs774048414, rs1274808359, rs774048743, rs1595826673, rs398123149, rs886042439, rs2052593499, rs761257703, rs727503837, rs750443041, rs768374736, rs398123143, rs1555422832, rs863224960, rs775130589, rs753360208, rs1555420765, rs776043976, rs770894443, rs1085307995, rs863224966, rs778768583, rs886043752, rs139836397, rs2054186817, rs863224958, rs754761503, rs80338803, rs1057524468, rs863224961, rs369784333, rs121434544, rs1555421854, rs587780289, rs773827877, rs746075428, rs777483913, rs1555421271, rs374665929, rs766917640, rs886041335, rs1555420462, rs794727697, rs761935462, rs773001194, rs1555423046, rs1366387924, rs199806879, rs1162942997, rs1555420507, rs794726871, rs886042557, rs1555417271, rs863224962, rs863224963, rs1293496023, rs587780290, rs886042895, rs528417986, rs747557404, rs398123146, rs121434545, rs868791726, rs557164942, rs886043432, rs1345121557, rs886042108, rs797045427, rs768090444, rs878854364	N/A
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy type 2A, Autosomal recessive limb-girdle muscular dystrophy, Limb-girdle muscular dystrophy	rs121434546, rs369552114, rs1275289254, rs1595844413, rs752848213, rs727503839, rs776059672, rs766334893, rs762471207, rs1566983844, rs886043432, rs1334369407, rs201736037, rs764459544, rs1555421263, rs863224957, rs1409503203, rs1555420475, rs749099493, rs1801505, rs1595845459, rs886044004, rs1459288402, rs149095128, rs768090444, rs750083132, rs886039597, rs764086484, rs121434547, rs863224965, rs886044475, rs1555422839, rs886042964, rs1555423015, rs1555422293, rs1555420075, rs1274808359, rs376107921, rs1595846922, rs886044052, rs777323132, rs761211705, rs779701414, rs886042418, rs1555420642, rs1595847257, rs886044527, rs1555422847, rs1555423222, rs794727318, rs1566984441, rs781013226, rs768374736, rs886042478, rs1555422298, rs863224959, rs774048414, rs769688710, rs200646556, rs774048743, rs1595826673, rs1555421280, rs398123149, rs1555420765, rs1555420647, rs1555423217, rs886042439, rs2052593499, rs761257703, rs1555422856, rs727503837, rs750443041, rs398123143, rs1555422832, rs863224960, rs200379491, rs80338804, rs775130589, rs1555421293, rs753360208, rs776043976, rs770894443, rs1085307995, rs267606703, rs758058910, rs863224966, rs777636094, rs1566965806, rs1555421523, rs778768583, rs886043752, rs139836397, rs2054186817, rs369784333, rs80338802, rs761897806, rs1555420634, rs863224958, rs1555421842, rs398123150, rs754761503, rs80338803, rs886042440, rs2053401167, rs1057524468, rs1555423027, rs1555421524, rs886042108, rs863224961, rs886041335, rs121434544, rs149914792, rs1595837172, rs1555421854, rs587780289, rs773827877, rs746075428, rs777483913, rs1555421271, rs1555420468, rs374665929, rs2053442769, rs766917640, rs794726871, rs1555420462, rs794727697, rs761935462, rs773001194, rs1555423046, rs201892814, rs1555423021, rs1457010016, rs1366387924, rs1595794433, rs199806879, rs1162942997, rs80338800, rs528417986, rs1555420507, rs1566975090, rs1064793620, rs886042557, rs1555417271, rs863224962, rs901764287, rs868791726, rs863224963, rs1595828703, rs1293496023, rs587780290, rs760205277, rs1555421847, rs121434548, rs763719290, rs1555421871, rs142004418, rs1595821204, rs747557404, rs1555417257, rs398123146, rs1555422954, rs121434545, rs745967703, rs1555421532, rs147764579, rs557164942, rs1566975163, rs746935735, rs1345121557, rs863224956, rs2053485642, rs1555423146, rs797045427, rs781723572, rs1555417321, rs886042573, rs1555420302, rs878854364, rs760919949, rs863224964, rs767739787, rs886042895, rs80338801, rs2053509916, rs1085307534, rs1447774727, rs766156798, rs147774793, rs1595838545, rs1555420083	N/A

Unknown
Disease merge term	Disease name	Evidence	References	Source
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Alzheimer Disease	Associate	28881388, 32854783
Aphasia	Associate	34355366
Chromosome Aberrations	Associate	39973406
Clubfoot	Associate	31991774
Conduct Disorder	Associate	31788660
Contracture	Associate	26632398, 31991774
Developmental Disabilities	Associate	16415965
Distal Myopathies	Associate	12145747
Dysferlinopathy	Associate	22825607
Dyspnea	Associate	29685414
Dystonia 18	Associate	37589857
Facioscapulohumeral muscular dystrophy 1a	Associate	33386810
Fatigue Syndrome Chronic	Associate	37589857
Glycogen Storage Disease Type II	Associate	31931849
Heat Stress Disorders	Associate	39457051
Hypomagnesemia primary	Associate	12890817, 21172462, 40226307
Immunologic Deficiency Syndromes	Associate	22825607
Limb girdle muscular dystrophy autosomal recessive	Associate	34863162
Limb girdle muscular dystrophy type 2A	Associate	10330340, 12482600, 12801918, 12890817, 14578192, 15073171, 16100770, 16141003, 16542520, 16971480, 17596655, 19015733, 20139084, 20634290, 20739790, 21172462, 22057634, 22378277, 22443334, 23597518, 25079074, 25135358, 26632398, 26677118, 28103310, 28881388, 29382717, 31498126, 31788660, 31937337, 31991774, 33386810, 34355366, 38104240, 40226307, 9150160
Limb girdle muscular dystrophy type 2B	Inhibit	34298987
Lipoma	Associate	31555977
Lymphedema Congenital Recessive	Associate	31931849
Melanoma	Associate	25658320, 26489459
Mobility Limitation	Associate	34355366
Muscle Rigidity	Associate	31991774
Muscle Weakness	Associate	34863162, 35741838, 37589857, 40226307
Muscular Atrophy	Associate	12181300, 22443334
Muscular Diseases	Associate	20489141, 35239206
Muscular Diseases	Inhibit	29685414
Muscular Dystrophies	Associate	19835634, 22825607, 31991774, 34628793, 35790299, 37589857, 9150160
Muscular Dystrophies Limb Girdle	Associate	11077661, 16100969, 17596655, 20634290, 22057634, 22311686, 27142102, 27708273, 28881388, 29685414, 29970176, 31498126, 31612648, 31991774, 33337384, 33386810, 33862537, 33899113, 34863162, 35239206, 37688281, 39973406, 40226307, 8320700
Muscular Dystrophy Duchenne	Associate	22825607
Muscular Dystrophy Emery Dreifuss	Associate	31991774
Muscular Dystrophy Facioscapulohumeral	Associate	22079131
Muscular Dystrophy Limb Girdle Type 2J	Associate	20634290
Myositis Inclusion Body	Associate	19291799, 28330496
Neoplasm Metastasis	Associate	25658320
Neoplasms	Inhibit	35790299
Nerve Degeneration	Associate	12890817, 22443334
Neuromuscular Diseases	Associate	22825607
Neuronal Ceroid Lipofuscinoses	Associate	15719035, 16415965, 30541466
Osteogenesis imperfecta type 2A	Associate	9150160
Respiratory Insufficiency	Associate	29685414
Retinal Dystrophies	Associate	34298987
Sarcoglycanopathies	Associate	22825607
Sprengel deformity	Associate	26632398