U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PMPCA peptidase, mitochondrial processing subunit alpha [ Homo sapiens (human) ]

Gene ID: 23203, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
PMPCAprovided by HGNC
Official Full Name
peptidase, mitochondrial processing subunit alphaprovided by HGNC
Primary source
HGNC:HGNC:18667
See related
Ensembl:ENSG00000165688 MIM:613036; AllianceGenome:HGNC:18667
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLA1; CPD3; MAS2; P-55; SCAR2; INPP5E; Alpha-MPP
Summary
The protein encoded by this gene is found in the mitochondrion, where it represents the alpha subunit of a proteolytic heterodimer. This heterodimer is responsible for cleaving the transit peptide from nuclear-encoded mitochondrial proteins. Defects in this gene are a cause of spinocerebellar ataxia, autosomal recessive 2. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in heart (RPKM 12.6), testis (RPKM 12.5) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
9q34.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136410658..136423761)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148639988..148653102)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139305110..139318213)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small nuclear RNA activating complex polypeptide 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139291906-139293105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139294835-139295771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139301375-139301963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29309 Neighboring gene endosome associated trafficking regulator 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139310410-139311609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139330456-139330964 Neighboring gene inositol polyphosphate-5-phosphatase E Neighboring gene hESC enhancers GRCh37_chr9:139332501-139333134 to GRCh37_chr9:139333770-139334403 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:139342099-139343298 Neighboring gene SEC16 homolog A, endoplasmic reticulum export factor Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:139376640-139377385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139378131-139378875 Neighboring gene chromosome 9 putative open reading frame 163

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Next-Generation Sequencing Identifies Novel PMPCA Variants in Patients with Late-Onset Dominant Optic Atrophy. Charif M, et al. Genes (Basel), 2022 Jul 5. PMID 35885985, Free PMC Article
  2. A severe form of autosomal recessive spinocerebellar ataxia associated with novel PMPCA variants. Takahashi Y, et al. Brain Dev, 2021 Mar. PMID 33272776
  3. Autosomal recessive cerebellar ataxia caused by a homozygous mutation in PMPCA. Choquet K, et al. Brain, 2016 Mar. PMID 26657514
  4. A polymorphism exon 1 variant at the locus of the scavenger receptor class B type I (SCARB1) gene is associated with differences in insulin sensitivity in healthy people during the consumption of an olive oil-rich diet. Pérez-Martínez P, et al. J Clin Endocrinol Metab, 2005 Apr. PMID 15671101
  5. Autosomal recessive congenital cerebellar hypoplasia and short stature in a large inbred family. Mégarbané A, et al. Am J Med Genet, 1999 Nov 5. PMID 10528257

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Next-Generation Sequencing Identifies Novel PMPCA Variants in Patients with Late-Onset Dominant Optic Atrophy.
    Title: Next-Generation Sequencing Identifies Novel PMPCA Variants in Patients with Late-Onset Dominant Optic Atrophy.
  2. A severe form of autosomal recessive spinocerebellar ataxia associated with novel PMPCA variants.
    Title: A severe form of autosomal recessive spinocerebellar ataxia associated with novel PMPCA variants.
  3. Functional coupling of presequence processing and degradation in human mitochondria.
    Title: Functional coupling of presequence processing and degradation in human mitochondria.
  4. Observational study of gene-environment interaction. (HuGE Navigator)
    Title: A polymorphism exon 1 variant at the locus of the scavenger receptor class B type I (SCARB1) gene is associated with differences in insulin sensitivity in healthy people during the consumption of an olive oil-rich diet.
  5. study represents the first time that defects in PMPCA and mitochondrial processing peptidase have been described in association with a disease phenotype in humans.
    Title: PMPCA mutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia.
  6. OxLDL triggers retrograde translocation of arginase2 in aortic endothelial cells via ROCK and mitochondrial processing peptidase.
    Title: OxLDL triggers retrograde translocation of arginase2 in aortic endothelial cells via ROCK and mitochondrial processing peptidase.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive spinocerebellar ataxia 2
MedGen: C1859298 OMIM: 213200 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ26258, KIAA0123, MGC104197

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloendopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein processing involved in protein targeting to mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein processing involved in protein targeting to mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein processing involved in protein targeting to mitochondrion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein processing involved in protein targeting to mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular space HDA PubMed 
located_in mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
  
part_of mitochondrial processing peptidase complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
mitochondrial-processing peptidase subunit alpha
Names
Cerebellar ataxia-1
cerebellar ataxia 1 (autosomal recessive)
inactive zinc metalloprotease alpha
inositol polyphosphate-5-phosphatase, 72 kD
mitochondrial matrix processing protease, alpha subunit
peptidase, mitochondrial processing alpha subunit
NP_001269873.1
NP_001269875.1
NP_055975.1
XP_005266116.1
XP_011516719.1
XP_054218487.1
XP_054218488.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_046789.1 RefSeqGene

    Range
    5086..18189
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282944.2 → NP_001269873.1  mitochondrial-processing peptidase subunit alpha isoform 2

    See identical proteins and their annotated locations for NP_001269873.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' coding region which results in the use of a alternate start codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA037280, AK296617, AL592301
    UniProtKB/Swiss-Prot
    Q10713
    Conserved Domains (3) summary
    COG0612
    Location:69 → 373
    PqqL; Predicted Zn-dependent peptidase [General function prediction only]
    pfam00675
    Location:47 → 96
    Peptidase_M16; Insulinase (Peptidase family M16)
    pfam05193
    Location:101 → 300
    Peptidase_M16_C; Peptidase M16 inactive domain

  2. NM_001282946.2 → NP_001269875.1  mitochondrial-processing peptidase subunit alpha isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region which results in the use of an alternate start codon compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK308104, AL592301, BC022949
    UniProtKB/Swiss-Prot
    Q10713
    Conserved Domains (3) summary
    COG0612
    Location:47 → 404
    PqqL; Predicted Zn-dependent peptidase [General function prediction only]
    pfam00675
    Location:35 → 127
    Peptidase_M16; Insulinase (Peptidase family M16)
    pfam05193
    Location:132 → 331
    Peptidase_M16_C; Peptidase M16 inactive domain

  3. NM_015160.3 → NP_055975.1  mitochondrial-processing peptidase subunit alpha isoform 1 precursor

    See identical proteins and their annotated locations for NP_055975.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL592301, BC022949
    Consensus CDS
    CCDS35180.1
    UniProtKB/Swiss-Prot
    B4DKL3, E7ET61, Q10713, Q16639, Q5SXM9, Q8N513
    UniProtKB/TrEMBL
    A0A994J5K1
    Related
    ENSP00000360782.3, ENST00000371717.8
    Conserved Domains (1) summary
    COG0612
    Location:65 → 504
    PqqL; Predicted Zn-dependent peptidase [General function prediction only]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    136410658..136423761
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005266059.4 → XP_005266116.1  mitochondrial-processing peptidase subunit alpha isoform X1

    UniProtKB/TrEMBL
    A0A994J5K1, Q5SXN9
    Related
    ENSP00000408393.2, ENST00000444897.3
    Conserved Domains (3) summary
    COG0612
    Location:65 → 465
    PqqL; Predicted Zn-dependent peptidase [General function prediction only]
    pfam00675
    Location:77 → 227
    Peptidase_M16; Insulinase (Peptidase family M16)
    pfam05193
    Location:232 → 431
    Peptidase_M16_C; Peptidase M16 inactive domain

  2. XM_011518417.4 → XP_011516719.1  mitochondrial-processing peptidase subunit alpha isoform X2

    Conserved Domains (3) summary
    COG0612
    Location:18 → 283
    PqqL; Predicted Zn-dependent peptidase [General function prediction only]
    pfam00675
    Location:1 → 45
    Peptidase_M16; Insulinase (Peptidase family M16)
    pfam05193
    Location:50 → 249
    Peptidase_M16_C; Peptidase M16 inactive domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148639988..148653102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362512.1 → XP_054218487.1  mitochondrial-processing peptidase subunit alpha isoform X1

    UniProtKB/TrEMBL
    Q5SXN9

  2. XM_054362513.1 → XP_054218488.1  mitochondrial-processing peptidase subunit alpha isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q10713.2 GenPept UniProtKB/Swiss-Prot:Q10713

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous