Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1201
Gene name	CLN3 lysosomal/endosomal transmembrane protein, battenin
Gene symbol	CLN3
Synonyms (NCBI Gene)	BTN1BTSJNCLSLC29B1
Chromosome	16
Chromosome location	16p12.1
Summary	This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid

Show/Hide all (93)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1142183	C>T	Benign-likely-benign, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs121434286	C>A,T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant, stop gained
rs137906617	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, stop gained, missense variant
rs139842473	G>A,C,T	Likely-pathogenic, likely-benign, uncertain-significance	Synonymous variant, coding sequence variant, missense variant
rs142456044	G>A,C	Likely-pathogenic	Coding sequence variant, stop gained, synonymous variant
rs147667964	G>A,C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs201206239	C>T	Benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs267606737	G>T	Likely-pathogenic, pathogenic	Stop gained, coding sequence variant
rs386833694	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs386833695	C>T	Pathogenic-likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs386833696	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833697	G>A	Pathogenic-likely-pathogenic, pathogenic	Coding sequence variant, stop gained
rs386833698	T>G	Likely-pathogenic	Intron variant
rs386833699	C>A,G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833700	C>T	Likely-pathogenic, pathogenic	Intron variant, coding sequence variant, stop gained
rs386833701	C>A,G	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs386833702	C>A	Pathogenic	Splice acceptor variant
rs386833703	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833704	C>T	Likely-pathogenic	Intron variant
rs386833705	C>T	Likely-pathogenic	Splice acceptor variant
rs386833706	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs386833707	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833708	T>C,G	Likely-pathogenic	Missense variant, 5 prime UTR variant, initiator codon variant
rs386833709	G>A	Likely-pathogenic, pathogenic	5 prime UTR variant, coding sequence variant, stop gained
rs386833710	A>C	Likely-pathogenic	Splice donor variant
rs386833711	C>G	Likely-pathogenic	Intron variant
rs386833712	->C	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs386833713	G>A	Likely-pathogenic	Intron variant, synonymous variant, coding sequence variant, stop gained
rs386833714	A>G	Likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs386833715	->A	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs386833716	C>T	Likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs386833717	G>-,GGG	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs386833719	A>C,G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833720	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs386833721	C>A,G,T	Likely-pathogenic	Intron variant
rs386833722	C>A,G,T	Likely-pathogenic	Splice acceptor variant
rs386833723	C>G,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs386833724	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs386833725	G>C	Likely-pathogenic	Coding sequence variant, stop gained
rs386833726	C>A,T	Likely-pathogenic, uncertain-significance	Intron variant, coding sequence variant, stop gained, missense variant
rs386833727	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833728	C>G,T	Likely-pathogenic	Splice donor variant
rs386833729	CT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833730	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs386833731	C>A,G,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs386833732	C>-,CC	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs386833733	C>T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs386833735	C>-,CC	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833736	->A	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs386833737	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs386833738	T>G	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Intron variant
rs386833739	C>T	Likely-pathogenic	Intron variant
rs386833740	->T	Pathogenic	Frameshift variant, coding sequence variant
rs386833741	CCTCGCTCCTCTTACCAGCGGTATTGC>-	Likely-pathogenic	Splice donor variant, coding sequence variant, intron variant
rs386833742	C>A,T	Likely-pathogenic	Splice acceptor variant
rs386833743	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs386833744	C>A,T	Likely-pathogenic, uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs587779397	->A	Pathogenic	Frameshift variant, intron variant, coding sequence variant
rs748710466	C>-	Pathogenic	Frameshift variant, intron variant, coding sequence variant
rs748844685	T>C	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs756848924	C>T	Uncertain-significance, likely-pathogenic	Intron variant
rs764999720	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs765157752	G>C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs771788391	A>T	Pathogenic, likely-pathogenic	Splice donor variant
rs777625354	A>G	Likely-pathogenic	5 prime UTR variant, missense variant, initiator codon variant
rs786201028	C>T	Pathogenic	Coding sequence variant, missense variant
rs796052335	G>A	Pathogenic	Coding sequence variant, stop gained
rs796052336	T>A	Likely-pathogenic	Intron variant
rs886041546	CC>-	Pathogenic	Frameshift variant, coding sequence variant
rs886043242	C>-	Pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516267	C>T	Likely-pathogenic	Splice donor variant
rs1057516335	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057516343	C>G,T	Likely-pathogenic	Splice donor variant
rs1057516677	G>T	Likely-pathogenic, pathogenic	Stop gained, coding sequence variant
rs1057517215	AG>-	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant
rs1057517287	C>A	Likely-pathogenic	Splice donor variant
rs1057517350	C>T	Likely-pathogenic	Splice acceptor variant
rs1064794233	T>A	Pathogenic	Stop gained, coding sequence variant
rs1064795153	G>-	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1064796502	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1418997146	T>G	Likely-pathogenic	Splice acceptor variant
rs1478660606	T>G	Likely-pathogenic	Intron variant, splice acceptor variant
rs1555467473	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555468374	C>-	Likely-pathogenic	Splice donor variant, coding sequence variant
rs1555468632	TTGCAATCATAATCAAGTTTTCTTTTCTTTCTTTTTTTTTTTTTCTTCCTGAGACAGAGTCTAACTCTGTCGCCCGGGCTGGAGTGCAATGGCACGATCTCGGCTCACTGCCACCACTGCCTCCGGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCTGAGTAGTTGGGACTACAGGCACCCGCCACCACACCTGGCTAATTGTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTTCCTG	Pathogenic, likely-pathogenic	Coding sequence variant, splice donor variant, intron variant, splice acceptor variant
rs1555468634	ATTGCAATCATAATCAAGTTTTCTTTTCTTTCTTTTTTTTTTTTTCTTCCTGAGACAGAGTCTAACTCTGTCGCCCGGGCTGGAGTGCAATGGCACGATCTCGGCTCACTGCCACCACTGCCTCCGGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCTGAGTAGTTGGGACTACAGGCACCCGCCACCACACCTGGCTAATTGTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTTCCT	Pathogenic	Coding sequence variant, splice donor variant, intron variant, splice acceptor variant
rs1555468920	A>-	Likely-pathogenic	Frameshift variant, intron variant, coding sequence variant
rs1555469089	C>T	Likely-pathogenic	Intron variant, splice acceptor variant
rs1555469159	->G	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1555469452	C>-	Likely-pathogenic	Splice donor variant, intron variant, coding sequence variant
rs1555469477	C>T	Uncertain-significance, likely-pathogenic	Intron variant, splice acceptor variant
rs1596556924	T>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1596563048	T>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant

Show/Hide all (10)

miRTarBase ID	miRNA	Experiments	Reference
MIRT025765	hsa-miR-7-5p	Microarray	19073608
MIRT037057	hsa-miR-877-3p	CLASH	23622248
MIRT897027	hsa-miR-2276	CLIP-seq
MIRT897028	hsa-miR-3652	CLIP-seq
MIRT897029	hsa-miR-4261	CLIP-seq
MIRT897030	hsa-miR-4430	CLIP-seq
MIRT897031	hsa-miR-4505	CLIP-seq
MIRT897032	hsa-miR-4708-3p	CLIP-seq
MIRT897033	hsa-miR-4755-3p	CLIP-seq
MIRT2447200	hsa-miR-3162-3p	CLIP-seq

158

Show/Hide all (158)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IDA	9949212, 10191111
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0001508	Process	Action potential	IEA
GO:0001508	Process	Action potential	ISS
GO:0005515	Function	Protein binding	IPI	12134079, 14699076, 15471887, 15598649, 17189291, 17237713, 19941651, 20015955, 20850431, 22261744, 32814053
GO:0005634	Component	Nucleus	IDA	10191116
GO:0005737	Component	Cytoplasm	IDA	10191116
GO:0005764	Component	Lysosome	IBA
GO:0005764	Component	Lysosome	IDA	10332042, 10924275, 14699076, 15471887, 19941651
GO:0005764	Component	Lysosome	IEA
GO:0005764	Component	Lysosome	IMP	14644441
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005765	Component	Lysosomal membrane	IDA	9384607, 10332042
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	IMP	15598649, 23840424
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IDA	15240864
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IDA	10332042, 15471887, 22261744
GO:0005770	Component	Late endosome	IEA
GO:0005770	Component	Late endosome	IMP	23840424
GO:0005770	Component	Late endosome	ISS
GO:0005776	Component	Autophagosome	IEA
GO:0005776	Component	Autophagosome	ISS
GO:0005783	Component	Endoplasmic reticulum	IDA	10191111
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	12706816
GO:0005794	Component	Golgi apparatus	IDA	10332042, 15240864
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	IMP	23840424
GO:0005795	Component	Golgi stack	IDA	15240864
GO:0005795	Component	Golgi stack	IEA
GO:0005802	Component	Trans-Golgi network	IDA	10332042, 15240864
GO:0005802	Component	Trans-Golgi network	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005886	Component	Plasma membrane	IDA	10191116, 15240864
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	IMP	14644441
GO:0005901	Component	Caveola	IDA	15240864
GO:0005901	Component	Caveola	IEA
GO:0005901	Component	Caveola	IMP	23840424
GO:0006865	Process	Amino acid transport	IEA
GO:0006865	Process	Amino acid transport	IEA
GO:0006897	Process	Endocytosis	IEA
GO:0006897	Process	Endocytosis	IEA
GO:0006898	Process	Receptor-mediated endocytosis	IMP	15471887
GO:0007040	Process	Lysosome organization	IBA
GO:0007040	Process	Lysosome organization	IEA
GO:0007040	Process	Lysosome organization	IEA
GO:0007040	Process	Lysosome organization	ISS
GO:0007042	Process	Lysosomal lumen acidification	IBA
GO:0007042	Process	Lysosomal lumen acidification	IMP	11722572
GO:0007611	Process	Learning or memory	IEA
GO:0007611	Process	Learning or memory	ISS
GO:0008021	Component	Synaptic vesicle	IDA	10332042, 11590129
GO:0008306	Process	Associative learning	IEA
GO:0008306	Process	Associative learning	ISS
GO:0009992	Process	Intracellular water homeostasis	IEA
GO:0009992	Process	Intracellular water homeostasis	ISS
GO:0010506	Process	Regulation of autophagy	IEA
GO:0010762	Process	Regulation of fibroblast migration	IMP	20850431
GO:0016020	Component	Membrane	IDA	10191112
GO:0016020	Component	Membrane	IEA
GO:0016236	Process	Macroautophagy	IEA
GO:0016243	Process	Regulation of autophagosome size	IEA
GO:0016485	Process	Protein processing	IEA
GO:0016485	Process	Protein processing	ISS
GO:0017089	Function	Glycolipid transfer activity	TAS
GO:0030003	Process	Intracellular monoatomic cation homeostasis	IEA
GO:0030036	Process	Actin cytoskeleton organization	IEA
GO:0030162	Process	Regulation of proteolysis	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031901	Component	Early endosome membrane	IEA
GO:0031901	Component	Early endosome membrane	IMP	23840424
GO:0031902	Component	Late endosome membrane	IEA
GO:0032228	Process	Regulation of synaptic transmission, GABAergic	IEA
GO:0032228	Process	Regulation of synaptic transmission, GABAergic	ISS
GO:0035235	Process	Ionotropic glutamate receptor signaling pathway	IEA
GO:0035235	Process	Ionotropic glutamate receptor signaling pathway	ISS
GO:0035627	Process	Ceramide transport	TAS
GO:0035752	Process	Lysosomal lumen pH elevation	IDA	10924275
GO:0036359	Process	Renal potassium excretion	IEA
GO:0036359	Process	Renal potassium excretion	ISS
GO:0042987	Process	Amyloid precursor protein catabolic process	IDA	10924275
GO:0042998	Process	Positive regulation of Golgi to plasma membrane protein transport	IEA
GO:0042998	Process	Positive regulation of Golgi to plasma membrane protein transport	ISS
GO:0043005	Component	Neuron projection	IDA	10332042
GO:0043005	Component	Neuron projection	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IMP	15240864
GO:0043066	Process	Negative regulation of apoptotic process	ISS
GO:0043524	Process	Negative regulation of neuron apoptotic process	IEA
GO:0043524	Process	Negative regulation of neuron apoptotic process	ISS
GO:0043534	Process	Blood vessel endothelial cell migration	IEA
GO:0044754	Component	Autolysosome	IEA
GO:0044754	Component	Autolysosome	ISS
GO:0044857	Process	Plasma membrane raft organization	IEA
GO:0044857	Process	Plasma membrane raft organization	ISS
GO:0045121	Component	Membrane raft	IDA	15240864
GO:0045121	Component	Membrane raft	IEA
GO:0045121	Component	Membrane raft	IMP	23840424
GO:0045202	Component	Synapse	IEA
GO:0045861	Process	Negative regulation of proteolysis	IEA
GO:0045861	Process	Negative regulation of proteolysis	ISS
GO:0046474	Process	Glycerophospholipid biosynthetic process	IMP	17482562
GO:0046836	Process	Glycolipid transport	IMP	18317235
GO:0047496	Process	Vesicle transport along microtubule	IMP	22261744
GO:0048172	Process	Regulation of short-term neuronal synaptic plasticity	IEA
GO:0048172	Process	Regulation of short-term neuronal synaptic plasticity	ISS
GO:0048306	Function	Calcium-dependent protein binding	IEA
GO:0048549	Process	Positive regulation of pinocytosis	IEA
GO:0048549	Process	Positive regulation of pinocytosis	ISS
GO:0050885	Process	Neuromuscular process controlling balance	IEA
GO:0050885	Process	Neuromuscular process controlling balance	ISS
GO:0051480	Process	Regulation of cytosolic calcium ion concentration	IEA
GO:0051480	Process	Regulation of cytosolic calcium ion concentration	ISS
GO:0051489	Process	Regulation of filopodium assembly	IEA
GO:0051493	Process	Regulation of cytoskeleton organization	IMP	20850431
GO:0051649	Process	Establishment of localization in cell	IEA
GO:0051649	Process	Establishment of localization in cell	IEA
GO:0051861	Function	Glycolipid binding	IDA	18317235
GO:0051966	Process	Regulation of synaptic transmission, glutamatergic	IEA
GO:0051966	Process	Regulation of synaptic transmission, glutamatergic	ISS
GO:0055037	Component	Recycling endosome	IDA	15240864
GO:0055037	Component	Recycling endosome	IEA
GO:0061024	Process	Membrane organization	IEA
GO:0061024	Process	Membrane organization	IEA
GO:0061024	Process	Membrane organization	ISS
GO:0061909	Process	Autophagosome-lysosome fusion	IEA
GO:0061909	Process	Autophagosome-lysosome fusion	ISS
GO:0065008	Process	Regulation of biological quality	IEA
GO:0070613	Process	Regulation of protein processing	IMP	10924275
GO:0072657	Process	Protein localization to membrane	IEA
GO:0072659	Process	Protein localization to plasma membrane	IEA
GO:0090160	Process	Golgi to lysosome transport	IMP	18817525
GO:0090384	Process	Phagosome-lysosome docking	IEA
GO:0090384	Process	Phagosome-lysosome docking	ISS
GO:0090385	Process	Phagosome-lysosome fusion	IEA
GO:0090385	Process	Phagosome-lysosome fusion	ISS
GO:0097352	Process	Autophagosome maturation	IEA
GO:0097352	Process	Autophagosome maturation	ISS
GO:0106049	Process	Regulation of cellular response to osmotic stress	IMP	23840424
GO:0120146	Function	Sulfatide binding	IDA	18317235
GO:1900079	Process	Regulation of arginine biosynthetic process	IEA
GO:1900079	Process	Regulation of arginine biosynthetic process	ISS
GO:1901096	Process	Regulation of autophagosome maturation	IEA
GO:1901096	Process	Regulation of autophagosome maturation	ISS
GO:1903076	Process	Regulation of protein localization to plasma membrane	IEA
GO:1903076	Process	Regulation of protein localization to plasma membrane	ISS
GO:1903826	Process	L-arginine transmembrane transport	IDA	16251196
GO:1905146	Process	Lysosomal protein catabolic process	IEA
GO:1905146	Process	Lysosomal protein catabolic process	ISS
GO:1905162	Process	Regulation of phagosome maturation	IEA
GO:1905162	Process	Regulation of phagosome maturation	ISS
GO:1905244	Process	Regulation of modification of synaptic structure	IEA
GO:1905244	Process	Regulation of modification of synaptic structure	ISS
GO:2001288	Process	Positive regulation of caveolin-mediated endocytosis	IEA
GO:2001288	Process	Positive regulation of caveolin-mediated endocytosis	ISS

MIM	HGNC	e!Ensembl
607042	2074	ENSG00000188603

Q13286

Protein name

Battenin (Batten disease protein) (Protein CLN3)

Protein function

Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein deg

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02487	CLN3	39 → 437	CLN3 protein	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in the cortical brain, pancreas, spleen, and testis with weaker expression in the peripheral nerve (at protein level). Highly expressed in gray matter (at protein level). {ECO:0000269|PubMed:10191116}.

Sequence

MGGCAGSRRRFSDSEGEETVPEPRLPLLDHQGAHWKNAVGFWLLGLCNNFSYVVMLSAAH
DILSHKRTSGNQSHVDPGPTPIPHNSSSRFDCNSVSTAAVLLADILPTLVIKLLAPLGLH
LLPYSPRVLVSGICAAGSFVLVAFSHSVGTSLCGVVFASISSGLGEVTFLSLTAFYPRAV
ISWWSSGTGGAGLLGALSYLGLTQAGLSPQQTLLSMLGIPALLLASYFLLLTSPEAQDPG
GEEEAESAARQPLIRTEAPESKPGSSSSLSLRERWTVFKGLLWYIVPLVVVYFAEYFINQ
GLFELLFFWNTSLSHAQQYRWYQMLYQAGVFASRSSLRCCRIRFTWALALLQCLNLVFLL
ADVWFGFLPSIYLVFLIILYEGLLGGAAYVNTFHNIALETSDEHREFAMAATCISDTLGI
SLSGLLALPLHDFLCQLS

Sequence length

438

Interactions

View interactions

	KEGG
	Lysosome

1370

Show/Hide Causal Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ceroid lipofuscinosis, neuronal, 3, protracted	Pathogenic	rs786201028, rs121434286, rs267606737	RCV000162326 RCV000003735 RCV000003736
Clear cell carcinoma of kidney	Pathogenic	rs121434286	RCV005887257
CLN3-related disorder	Likely pathogenic; Pathogenic	rs386833708	RCV003420170
Cone-rod dystrophy	Pathogenic	rs2046020472, rs2046113301	RCV001199455 RCV001199454
early onset and severe retinal dystrophy	Pathogenic	rs121434286	RCV001270479
Juvenile neuronal ceroid lipofuscinosis	Likely pathogenic; Pathogenic	rs2506483030, rs1064794233	RCV005616500 RCV005614409
Malignant tumor of urinary bladder	Likely pathogenic	rs386833706	RCV005890361
Neuronal ceroid lipofuscinosis	Likely pathogenic; Pathogenic	rs1397086223, rs1218568487, rs746674736, rs2141693746, rs2046109345, rs2141712336, rs2141714500, rs1228953213, rs1418465028, rs2141707084, rs2046218391, rs2141722729, rs2141704162, rs2141703433, rs1217725909 View all (81 more)	RCV002545033 RCV001379292 RCV001378965 RCV001390150 RCV001389676 RCV001385754 RCV001383264 RCV001384656 RCV001891503 RCV001981877 RCV001881320 RCV002007404 RCV002007566 RCV002016097 RCV001990458 RCV001938804 RCV001875545 RCV001961679 RCV000811923 RCV000823290 RCV002644413 RCV003112008 RCV003104286 RCV002596568 RCV002635544 RCV000812919 RCV002516983 RCV002820291 RCV002815571 RCV002833798 RCV002838904 RCV002861758 RCV002881369 RCV002961992 RCV003009773 RCV002994396 RCV003053724 RCV003055459 RCV003052339 RCV002282095 RCV003534000 RCV003534052 RCV003534072 RCV003531459 RCV003531830 RCV003531822 RCV003532497 RCV003648137 RCV003648223 RCV003648306 RCV003648447 RCV003648501 RCV003648967 RCV000989587 RCV001861373 RCV002523852 RCV001379345 RCV000559381 RCV003532139 RCV001060717 RCV001851209 RCV000540211 RCV001378087 RCV001868197 RCV005091925 RCV000778462 RCV000817490 RCV000805513 RCV000812096 RCV000588369 RCV000696638 RCV001853040 RCV001804785 RCV000819629 RCV001217036 RCV001380722 RCV003317069 RCV001051149 RCV002513684 RCV000812617 RCV003531947 RCV001199876 RCV001853041 RCV001384516 RCV000819681 RCV001853042 RCV001853043 RCV001853044 RCV001853045 RCV000555143 RCV001239013 RCV001055217 RCV000477605 RCV001035044 RCV001378302 RCV000989588 RCV001057311 RCV001057267 RCV001057880 RCV001862820 RCV001222663 RCV001219439 RCV001232547 RCV001225343 RCV001251423
Neuronal ceroid lipofuscinosis 3	Likely pathogenic; Pathogenic	rs2046109345, rs587779397, rs1418465028, rs2046218391, rs2141714554, rs2506482028, rs1294714405, rs2506448642, rs2506454042, rs2506484397, rs1443772167, rs1555468634, rs121434286, rs267606737, rs781617143 View all (100 more)	RCV003469762 RCV000087084 RCV005016769 RCV003470987 RCV002249366 RCV002308239 RCV002308345 RCV002307168 RCV002310327 RCV002310399 RCV002308399 RCV000003731 RCV000055839 RCV000169443 RCV003465993 RCV003466009 RCV005021783 RCV003465786 RCV001729444 RCV001729442 RCV003465838 RCV003465843 RCV003465858 RCV005019582 RCV004572695 RCV003136476 RCV001729499 RCV001729502 RCV003388914 RCV003468452 RCV003468453 RCV003468454 RCV003468455 RCV003468456 RCV003468457 RCV003468458 RCV003468459 RCV003468460 RCV003468461 RCV003468462 RCV003468464 RCV003468465 RCV003468466 RCV003468467 RCV004574133 RCV004575660 RCV004575661 RCV000410540 RCV000410762 RCV000409352 RCV000410383 RCV000412040 RCV000411858 RCV000410679 RCV000409322 RCV000409491 RCV000409421 RCV001253588 RCV001729612 RCV001729613 RCV000576750 RCV001729626 RCV000668016 RCV000666933 RCV000664968 RCV000664720 RCV000664643 RCV000672581 RCV000665318 RCV000665468 RCV000667804 RCV000670278 RCV000674867 RCV004569622 RCV003467458 RCV000049655 RCV000049656 RCV000049657 RCV000049658 RCV000049659 RCV000049660 RCV000049661 RCV000049662 RCV000049663 RCV000049664 RCV000049665 RCV000049666 RCV000049667 RCV000049668 RCV000049669 RCV000049670 RCV000049671 RCV000049673 RCV000049674 RCV000049675 RCV000049676 RCV000049678 RCV000049679 RCV000049681 RCV000049682 RCV000049683 RCV000049684 RCV000049686 RCV000049687 RCV000049688 RCV000049690 RCV000049691 RCV000049692 RCV000049693 RCV000049694 RCV000049695 RCV000049698 RCV000049699 RCV000049700 RCV000049702 RCV000049703 RCV000049704 RCV000049705 RCV000049706 RCV000049707 RCV000049708 RCV004569848 RCV001784607 RCV001376248 RCV001810499 RCV003469375 RCV003469396 RCV003469484 RCV001263873 RCV001291631
Retinal dystrophy	Pathogenic; Likely pathogenic	rs121434286, rs386833744, rs139842473, rs386833697, rs386833728, rs2046158549, rs765893479	RCV001074385 RCV004816316 RCV001075708 RCV004814987 RCV001075762 RCV001074167 RCV004813909
Retinitis pigmentosa	Pathogenic; Likely pathogenic	rs1555468634, rs386833744, rs139842473, rs1555468632, rs1555468920, rs386833717	RCV003324482 RCV000504655 RCV000504756 RCV000505074 RCV001199669 RCV000678540
Sarcoma	Likely pathogenic	rs1555469477	RCV005901480

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs28545628	RCV005903996
Cervical cancer	Likely benign	rs779793979	RCV005912739
Gastric cancer	Uncertain significance	rs767755377	RCV005924152
Intellectual disability	Likely benign; Uncertain significance	rs2046113354, rs752130042, rs1006236175	RCV001251940 RCV001251941 RCV001251942
Lung cancer	Benign	rs28545628	RCV005903999
Malignant tumor of esophagus	Likely benign	rs113317066	RCV005904083
Neuronal Ceroid-Lipofuscinosis, Dominant/Recessive	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	rs146610181, rs77595156, rs11552531, rs376907245, rs150913606, rs373034150, rs144770450, rs137906617, rs113845299, rs377369610, rs150986176, rs769358990, rs756848924, rs748293490, rs572212180 View all (17 more)	RCV000274494 RCV000371392 RCV000367477 RCV000355271 RCV000346618 RCV000345320 RCV000405250 RCV000300798 RCV000310613 RCV000330765 RCV000316657 RCV000373570 RCV000286126 RCV000315181 RCV000260744 RCV000361392 RCV000302287 RCV000263814 RCV000284676 RCV000353206 RCV000323062 RCV000264464 RCV000341070 RCV000270904 RCV000314285 RCV000393510 RCV000363027 RCV000376958 RCV000288277 RCV000402737 RCV000310368 RCV000324671
Ovarian serous cystadenocarcinoma	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs1596556713, rs200023908, rs756848924, rs28545628	RCV005924161 RCV005890622 RCV005894433 RCV005903998
Progressive myoclonic epilepsy type 3	Conflicting classifications of pathogenicity	rs137906617	RCV000791120
Squamous cell lung carcinoma	Likely benign	rs2141703178	RCV005934623
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity; Likely benign	rs561083322, rs367945307	RCV005897986 RCV005902016
Uterine carcinosarcoma	Likely benign	rs777779035	RCV005899557
Uterine corpus endometrial carcinoma	Uncertain significance; Likely benign; Benign	rs181995380, rs113317066, rs28545628	RCV005899637 RCV005904085 RCV005904000

Show/Hide Text Mining Associations (41)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
16p11.2 Deletion Syndrome	Associate	23860047
Atrophy	Associate	32441891
Blindness	Associate	30621751, 33507216
Carcinogenesis	Associate	26299671
Carcinoma Hepatocellular	Associate	37014321, 38114725
Cardiomyopathy Restrictive	Associate	33507216
Cognition Disorders	Associate	31888773, 36964447
Cone Rod Dystrophies	Associate	24154662, 28542676, 33507216
Congenital Abnormalities	Associate	24271013
Death	Associate	33547385
Epilepsy	Associate	21863212, 39950246
Genetic Diseases Inborn	Associate	10191120, 9618513
Hypertensive Retinopathy	Associate	30621751, 33497524
Lysosomal Storage Diseases	Associate	18817525, 19132115, 33547385, 34964690, 39959975
Macular Degeneration	Associate	36964447
Macular dystrophy concentric annular	Associate	36964447
Mental Disorders	Associate	31888773
Motor Disorders	Associate	35427884
Nerve Degeneration	Associate	17475770, 20933060, 26308342
Nervous System Diseases	Associate	28542676, 33547385
Neurodegenerative Diseases	Associate	11053386, 11699874, 14644441, 21863212, 28542676, 34964690, 36965618
Neurologic Manifestations	Associate	21863212
Neuronal Ceroid Lipofuscinoses	Associate	10191120, 10191121, 10384264, 10500178, 10964839, 11053386, 11339651, 12706816, 14644441, 14660799, 15269304, 16415964, 1746562, 17475770, 17482562 View all (45 more)
Night blindness congenital stationary	Associate	20933060
Obesity	Associate	26449484
Ovarian Neoplasms	Associate	26299671
Parkinsonian Disorders	Associate	11339651
Psychomotor Disorders	Associate	21863212
Psychotic Disorders	Associate	39950246
Refsum Disease Infantile	Associate	33507216, 36811936
Renal Insufficiency	Associate	9311735
Retinal Degeneration	Associate	10964839, 24154662, 28542676, 29753273, 32441891, 33507216
Retinal Diseases	Associate	26308342, 28542676, 33507216
Retinal Dystrophies	Associate	24625443, 32441891, 36912596
Retinitis Pigmentosa	Associate	24154662, 33507216
RHYNS syndrome	Associate	29753273
Seizures	Associate	31888773, 33550636
Thyroid Cancer Papillary	Associate	23539563
Vacuolar myopathy	Associate	24827497
Vision Disorders	Associate	21863212, 31888773, 33547385, 36964447, 8014971
Voice Disorders	Associate	30621751

CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin)