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

    Gene ID: 23203, updated on 28-Oct-2024

    Summary

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    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
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    Genomic context

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    See PMPCA in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136410658..136423761)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148639988..148653102)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. 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
    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. 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
    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 (83) 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

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    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 matrix TAS
    Traceable Author Statement
    more info
    		  
    part_of mitochondrial processing peptidase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrion HTP 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

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    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)

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    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_2024_08

    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.

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