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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5095
Gene name Gene Name - the full gene name approved by the HGNC.	Propionyl-CoA carboxylase subunit alpha
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PCCA
Synonyms (NCBI Gene) Gene synonyms aliases	-
Chromosome Chromosome number	13
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	13q32.3
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is the alpha subunit of the heterodimeric mitochondrial enzyme Propionyl-CoA carboxylase. PCCA encodes the biotin-binding region of this enzyme. Mutations in either PCCA or PCCB (encoding the beta subunit) lead to an enzym

Show/Hide all(81)

SNP ID	Visualize variation	Clinical significance	Consequence
rs118169528	G>T	Benign, conflicting-interpretations-of-pathogenicity	Intron variant, coding sequence variant, missense variant, genic downstream transcript variant, non coding transcript variant
rs121964957	A>C,G,T	Likely-benign, pathogenic	5 prime UTR variant, coding sequence variant, stop gained, missense variant, synonymous variant, non coding transcript variant
rs121964958	T>A	Pathogenic	Intron variant, missense variant, non coding transcript variant, coding sequence variant
rs137861347	T>A,C,G	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, initiator codon variant, coding sequence variant
rs138149179	C>T	Pathogenic	5 prime UTR variant, non coding transcript variant, stop gained, coding sequence variant
rs141371306	C>T	Pathogenic-likely-pathogenic	5 prime UTR variant, missense variant, non coding transcript variant, coding sequence variant
rs142646074	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, intron variant, genic downstream transcript variant, 3 prime UTR variant, coding sequence variant
rs202247814	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 5 prime UTR variant
rs202247815	T>C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 5 prime UTR variant
rs202247816	C>G	Pathogenic	Genic downstream transcript variant, intron variant, non coding transcript variant, stop gained, coding sequence variant
rs367615795	G>A,C	Likely-pathogenic	Splice acceptor variant
rs368047060	G>A,T	Uncertain-significance, likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 5 prime UTR variant
rs369982920	G>A	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant, 3 prime UTR variant, coding sequence variant, synonymous variant, non coding transcript variant
rs398123297	->T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs573607437	T>-,TT	Pathogenic	Frameshift variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs745571507	G>-	Pathogenic-likely-pathogenic	Frameshift variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs746286209	A>C	Pathogenic	Splice acceptor variant
rs752761437	G>A	Likely-pathogenic, pathogenic	Intron variant, splice donor variant
rs760387660	T>A	Pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, stop gained
rs760976198	AG>-	Pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, frameshift variant
rs761295534	G>A,T	Uncertain-significance, likely-pathogenic	Non coding transcript variant, coding sequence variant, intron variant, missense variant, synonymous variant
rs764045674	GTTTA>-	Pathogenic	Intron variant, splice donor variant
rs768703749	C>A,T	Pathogenic-likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained, intron variant, synonymous variant
rs768756825	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign	5 prime UTR variant, coding sequence variant, non coding transcript variant, synonymous variant
rs771438170	G>A	Pathogenic-likely-pathogenic	Non coding transcript variant, coding sequence variant, 3 prime UTR variant, intron variant, missense variant, genic downstream transcript variant
rs774457925	T>C	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs774738181	C>T	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs774949844	T>C	Pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs776281864	A>G	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs776496862	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant, non coding transcript variant
rs794726976	CTAAT>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs794727334	AGTA>-	Pathogenic	Genic downstream transcript variant, splice donor variant, intron variant
rs794727620	G>A	Pathogenic	Splice acceptor variant
rs796052018	G>A,C	Likely-pathogenic	Intron variant, coding sequence variant, missense variant, non coding transcript variant, stop gained, genic downstream transcript variant
rs796052019	G>A,T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs879253801	A>G	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs879253802	G>A,T	Pathogenic	Splice donor variant
rs879253803	G>C	Pathogenic-likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs879253805	A>G	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs879253806	AATG>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, non coding transcript variant
rs879253807	G>A	Pathogenic	Splice acceptor variant
rs879253808	G>T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs879253809	TA>-	Pathogenic	5 prime UTR variant, intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs879253810	G>A	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs879253811	T>G	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant, non coding transcript variant
rs879253812	A>-	Pathogenic	5 prime UTR variant, intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs886039751	A>G	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs886043045	G>A	Likely-pathogenic	Downstream transcript variant, splice donor variant, genic downstream transcript variant
rs972937270	G>C	Pathogenic	Splice donor variant
rs1064793224	G>A	Likely-pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs1194679272	C>T	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant, intron variant
rs1206838893	A>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant
rs1241896966	G>T	Likely-pathogenic	Non coding transcript variant, missense variant, stop gained, genic downstream transcript variant, coding sequence variant
rs1323994245	->C	Pathogenic	Intron variant, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant, frameshift variant, non coding transcript variant
rs1367867218	G>T	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1421021643	G>A	Likely-pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs1443858896	C>T	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, missense variant
rs1444049793	A>G	Likely-pathogenic, uncertain-significance	Missense variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs1467680142	A>G	Likely-pathogenic	Intron variant
rs1555298451	G>A	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant, intron variant
rs1555327702	A>-	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant, non coding transcript variant
rs1555327732	G>T	Likely-pathogenic	Genic downstream transcript variant, splice donor variant, intron variant, 3 prime UTR variant
rs1555331314	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant, non coding transcript variant
rs1555342593	T>C	Likely-pathogenic	Splice donor variant, intron variant
rs1555361758	C>-	Likely-pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, stop gained
rs1555400381	T>-	Pathogenic-likely-pathogenic	5 prime UTR variant, frameshift variant, coding sequence variant, non coding transcript variant
rs1555455109	C>G	Likely-pathogenic	Genic downstream transcript variant, intron variant
rs1594090133	G>ATT	Pathogenic	Intron variant, frameshift variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs1594099731	C>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs1594160545	A>T	Likely-pathogenic	Missense variant, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant, non coding transcript variant
rs1594413545	A>-	Pathogenic	Non coding transcript variant, 5 prime UTR variant, frameshift variant, coding sequence variant
rs1594413897	GT>-	Pathogenic	Non coding transcript variant, 5 prime UTR variant, frameshift variant, coding sequence variant
rs1594961338	->A	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, intron variant
rs1594961620	G>T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs1594992191	C>G	Pathogenic	Non coding transcript variant, 5 prime UTR variant, stop gained, coding sequence variant
rs1595032920	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs1595033018	C>T	Likely-pathogenic	Missense variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs1595202534	G>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs1595202607	CCT>-	Likely-pathogenic	Non coding transcript variant, inframe deletion, coding sequence variant, intron variant
rs1595236063	->T	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, intron variant
rs1595860868	G>A	Pathogenic	Genic downstream transcript variant, splice donor variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT029589	hsa-miR-26b-5p	Microarray	19088304
MIRT040742	hsa-miR-455-5p	CLASH	23622248
MIRT445558	hsa-miR-486-5p	PAR-CLIP	22100165
MIRT445556	hsa-miR-15b-3p	PAR-CLIP	22100165
MIRT445555	hsa-miR-4326	PAR-CLIP	22100165
MIRT445554	hsa-miR-155-5p	PAR-CLIP	22100165
MIRT445553	hsa-miR-1273e	PAR-CLIP	22100165
MIRT445552	hsa-miR-568	PAR-CLIP	22100165
MIRT445551	hsa-miR-7152-5p	PAR-CLIP	22100165
MIRT445558	hsa-miR-486-5p	PAR-CLIP	22100165
MIRT445556	hsa-miR-15b-3p	PAR-CLIP	22100165
MIRT445555	hsa-miR-4326	PAR-CLIP	22100165
MIRT445554	hsa-miR-155-5p	PAR-CLIP	22100165
MIRT445553	hsa-miR-1273e	PAR-CLIP	22100165
MIRT445552	hsa-miR-568	PAR-CLIP	22100165
MIRT445551	hsa-miR-7152-5p	PAR-CLIP	22100165
MIRT445558	hsa-miR-486-5p	PAR-CLIP	22100165
MIRT445556	hsa-miR-15b-3p	PAR-CLIP	22100165
MIRT445555	hsa-miR-4326	PAR-CLIP	22100165
MIRT445554	hsa-miR-155-5p	PAR-CLIP	22100165
MIRT445553	hsa-miR-1273e	PAR-CLIP	22100165
MIRT445552	hsa-miR-568	PAR-CLIP	22100165
MIRT445551	hsa-miR-7152-5p	PAR-CLIP	22100165
MIRT445558	hsa-miR-486-5p	PAR-CLIP	22100165
MIRT445556	hsa-miR-15b-3p	PAR-CLIP	22100165
MIRT445555	hsa-miR-4326	PAR-CLIP	22100165
MIRT445554	hsa-miR-155-5p	PAR-CLIP	22100165
MIRT445553	hsa-miR-1273e	PAR-CLIP	22100165
MIRT445552	hsa-miR-568	PAR-CLIP	22100165
MIRT445551	hsa-miR-7152-5p	PAR-CLIP	22100165
MIRT2062542	hsa-miR-4775	CLIP-seq
MIRT2290912	hsa-miR-1271	CLIP-seq
MIRT2290913	hsa-miR-129-5p	CLIP-seq
MIRT2290914	hsa-miR-182	CLIP-seq
MIRT2290915	hsa-miR-216a	CLIP-seq
MIRT2290916	hsa-miR-298	CLIP-seq
MIRT2290917	hsa-miR-3074-3p	CLIP-seq
MIRT2290918	hsa-miR-342-3p	CLIP-seq
MIRT2290919	hsa-miR-3647-3p	CLIP-seq
MIRT2290920	hsa-miR-4282	CLIP-seq
MIRT2290921	hsa-miR-513a-3p	CLIP-seq
MIRT2290922	hsa-miR-587	CLIP-seq
MIRT2290923	hsa-miR-922	CLIP-seq
MIRT2290924	hsa-miR-96	CLIP-seq
MIRT2588574	hsa-miR-147	CLIP-seq
MIRT2588575	hsa-miR-155	CLIP-seq
MIRT2588576	hsa-miR-22	CLIP-seq
MIRT2588577	hsa-miR-3190	CLIP-seq
MIRT2588578	hsa-miR-3646	CLIP-seq
MIRT2588579	hsa-miR-3664-5p	CLIP-seq
MIRT2588580	hsa-miR-4422	CLIP-seq
MIRT2588581	hsa-miR-4522	CLIP-seq
MIRT2588582	hsa-miR-609	CLIP-seq
MIRT2588576	hsa-miR-22	CLIP-seq
MIRT2588577	hsa-miR-3190	CLIP-seq
MIRT2588578	hsa-miR-3646	CLIP-seq
MIRT2588579	hsa-miR-3664-5p	CLIP-seq
MIRT2588581	hsa-miR-4522	CLIP-seq

Show/Hide all(28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004658	Function	Propionyl-CoA carboxylase activity	IBA
GO:0004658	Function	Propionyl-CoA carboxylase activity	IDA	6765947
GO:0004658	Function	Propionyl-CoA carboxylase activity	IEA
GO:0004658	Function	Propionyl-CoA carboxylase activity	IMP	8434582
GO:0005515	Function	Protein binding	IPI	20725044, 32296183, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	16023992
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	NAS	29033250
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006631	Process	Fatty acid metabolic process	NAS	29033250
GO:0009081	Process	Branched-chain amino acid metabolic process	NAS	29033250
GO:0009374	Function	Biotin binding	IEA
GO:0009374	Function	Biotin binding	TAS	3460076
GO:0016042	Process	Lipid catabolic process	IEA
GO:0016874	Function	Ligase activity	IEA
GO:0016885	Function	Ligase activity, forming carbon-carbon bonds	IEA
GO:0019626	Process	Short-chain fatty acid catabolic process	IC	6765947, 8434582
GO:0019899	Function	Enzyme binding	IPI	19157941
GO:0046872	Function	Metal ion binding	IEA
GO:1902494	Component	Catalytic complex	IPI	20725044

MIM	HGNC	e!Ensembl
232000	8653	ENSG00000175198

Protein

UniProt ID

P05165

Protein name

Propionyl-CoA carboxylase alpha chain, mitochondrial (PCCase subunit alpha) (EC 6.4.1.3) (Propanoyl-CoA:carbon dioxide ligase subunit alpha)

Protein function

This is one of the 2 subunits of the biotin-dependent propionyl-CoA carboxylase (PCC), a mitochondrial enzyme involved in the catabolism of odd chain fatty acids, branched-chain amino acids isoleucine, threonine, methionine, and valine and other

PDB

2CQY , 2JKU , 7YBU , 8XL3 , 8XL4 , 8XL5

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00289	Biotin_carb_N	62 → 171	Biotin carboxylase, N-terminal domain	Domain
PF02786	CPSase_L_D2	176 → 385	Carbamoyl-phosphate synthase L chain, ATP binding domain	Domain
PF02785	Biotin_carb_C	397 → 506	Biotin carboxylase C-terminal domain	Domain
PF18140	PCC_BT	525 → 653	Propionyl-coenzyme A carboxylase BT domain	Domain
PF00364	Biotin_lipoyl	660 → 727	Biotin-requiring enzyme	Domain

Sequence

MAGFWVGTAPLVAAGRRGRWPPQQLMLSAALRTLKHVLYYSRQCLMVSRNLGSVGYDPNE
KTFDKILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKS
YLNMDAIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIES
KLLAKKAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRD
GFRLSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVV
EEAPSIFLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPV
TECITGLDLVQEMIRVAKGYPLRHKQADIRINGWAVECRVYAEDPYKSFGLPSIGRLSQY
QEPLHLPGVRVDSGIQPGSDISIYYDPMISKLITYGSDRTEALKRMADALDNYVIRGVTH
NIALLREVIINSRFVKGDISTKFLSDVYPDGFKGHMLTKSEKNQLLAIASSLFVAFQLRA
QHFQENSRMPVIKPDIANWELSVKLHDKVHTVVASNNGSVFSVEVDGSKLNVTSTWNLAS
PLLSVSVDGTQRTVQCLSREAGGNMSIQFLGTVYKVNILTRLAAELNKFMLEKVTEDTSS
VLRSPMPGVVVAVSVKPGDAVAEGQEICVIEAMKMQNSMTAGKTGTVKSVHCQAGDTVGE
GDLLVELE

Sequence length

728

Interactions

View interactions

	KEGG		Reactome
	Valine, leucine and isoleucine degradation Glyoxylate and dicarboxylate metabolism Propanoate metabolism Metabolic pathways Carbon metabolism		Biotin transport and metabolism Defective HLCS causes multiple carboxylase deficiency Propionyl-CoA catabolism

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Propionic acidemia	propionic acidemia	rs879253801, rs1595860868, rs776281864, rs1594413897, rs752761437, rs776496862, rs1594175453, rs192171304, rs879253808, rs2047402577, rs1241896966, rs1421021643, rs573607437, rs2147483647, rs794727334 View all (75 more)	N/A
Pontoneocerebellar hypoplasia	Pontocerebellar hypoplasia type 2D	rs796052019	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Alzheimer disease	Alzheimer's disease or family history of Alzheimer's disease	N/A	N/A	GWAS
Atrial Fibrillation	Atrial fibrillation	N/A	N/A	GWAS
Myopia	Myopia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Abnormalities Drug Induced	Associate	32819290
Atrial Fibrillation	Associate	34827661
Biotin deficiency	Associate	15623830
Carcinoma Renal Cell	Associate	30793530
Death	Associate	33183246
Genetic Diseases Inborn	Associate	32819290, 8434582, 9683601
Methylmalonic acidemia	Associate	17966092, 31449969
Non Muscle Invasive Bladder Neoplasms	Associate	28344356
Propionic Acidemia	Associate	10353789, 10820128, 12757933, 15949719, 17966092, 25046265, 28925364, 31449969, 31916709, 32252659, 32819290, 32822967, 33128956, 33183246, 33725819, 33923806, 35331292, 9683601 View all (3 more)
Propionic Acidemia	Inhibit	2154743, 26740382, 3687944, 6614005, 8023851
Sjogren's Syndrome	Associate	29504848
Stomach Neoplasms	Associate	33881965

PCCA (propionyl-CoA carboxylase subunit alpha)