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Aliases for PMPCA Gene

Aliases for PMPCA Gene

  • Peptidase, Mitochondrial Processing Alpha Subunit 2 3 5
  • Inositol Polyphosphate-5-Phosphatase, 72 KD 2 3
  • EC 3.4.24.64 4 58
  • Alpha-MPP 3 4
  • INPP5E 3 4
  • P-55 3 4
  • Mitochondrial Matrix Processing Protease, Alpha Subunit 3
  • Mitochondrial-Processing Peptidase Subunit Alpha 3
  • Peptidase (Mitochondrial Processing) Alpha 2
  • Cerebellar Ataxia 1 (Autosomal Recessive) 3
  • Cerebellar Ataxia-1 3
  • KIAA0123 4
  • SCAR2 3
  • CLA1 3
  • CPD3 3
  • MPPA 4

External Ids for PMPCA Gene

Previous HGNC Symbols for PMPCA Gene

  • INPP5E

Previous GeneCards Identifiers for PMPCA Gene

  • GC09P132746
  • GC09P134662
  • GC09P136580
  • GC09P138424
  • GC09P139305
  • GC09P108764

Summaries for PMPCA Gene

Entrez Gene Summary for PMPCA Gene

  • 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]

GeneCards Summary for PMPCA Gene

PMPCA (Peptidase, Mitochondrial Processing Alpha Subunit) is a Protein Coding gene. Diseases associated with PMPCA include Spinocerebellar Ataxia, Autosomal Recessive 2 and Normal Pressure Hydrocephalus. Among its related pathways are Inositol phosphate metabolism (KEGG) and Mitochondrial protein import. GO annotations related to this gene include metalloendopeptidase activity. An important paralog of this gene is UQCRC2.

UniProtKB/Swiss-Prot for PMPCA Gene

  • Cleaves presequences (transit peptides) from mitochondrial protein precursors.

Gene Wiki entry for PMPCA Gene

Additional gene information for PMPCA Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PMPCA Gene

Genomics for PMPCA Gene

Regulatory Elements for PMPCA Gene

Enhancers for PMPCA Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H136227 1.4 FANTOM5 Ensembl ENCODE dbSUPER 10 -182.2 -182196 1 L3MBTL2 BHLHE40 ATF2 FOSL1 JUND CREB1 FOS FOSL2 QSOX2 SDCCAG3 PMPCA NOTCH1 PIR36610 GC09M136222
GH09H136224 1.4 Ensembl ENCODE dbSUPER 10 -184.8 -184845 3 HDGF RB1 ZSCAN4 ARID4B SIN3A ZNF2 RAD21 RFX5 HSF1 SCRT2 LHX3 NACC2 SDCCAG3 PMPCA QSOX2 OBP2A GC09M136222 PIR36610
GH09H136437 0.9 ENCODE 12.3 +28.7 28652 3 HDGF RB1 ZNF76 SIN3A GLIS2 ZNF143 KLF7 DEK EGR2 SMARCA5 SEC16A SNAPC4 PMPCA SDCCAG3 INPP5E GC09P136426
GH09H136510 1.5 FANTOM5 ENCODE dbSUPER 6.2 +101.1 101091 3 HDAC1 PKNOX1 ATF1 NFRKB ZBTB40 TCF12 ZNF766 GATA2 ATF7 ETV6 SNAPC4 RABL6 EGFL7 PMPCA INPP5E DNLZ FAM69B TRAF2 MIR4673 SEC16A
GH09H136441 0.7 ENCODE 12.2 +31.3 31274 0 GATAD2A FOXA2 FOXA3 MAX REST RAD21 GABPA YY1 JUND HNF4A PMPCA SDCCAG3 SEC16A GC09M136450 PIR54263 GC09M136482 PIR43963
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PMPCA on UCSC Golden Path with GeneCards custom track

Promoters for PMPCA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000243015 130 1801 HDGF MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 ZNF548

Genomic Location for PMPCA Gene

Chromosome:
9
Start:
136,410,570 bp from pter
End:
136,423,761 bp from pter
Size:
13,192 bases
Orientation:
Plus strand

Genomic View for PMPCA Gene

Genes around PMPCA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PMPCA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PMPCA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PMPCA Gene

Proteins for PMPCA Gene

  • Protein details for PMPCA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q10713-MPPA_HUMAN
    Recommended name:
    Mitochondrial-processing peptidase subunit alpha
    Protein Accession:
    Q10713
    Secondary Accessions:
    • B4DKL3
    • E7ET61
    • Q16639
    • Q5SXM9
    • Q8N513

    Protein attributes for PMPCA Gene

    Size:
    525 amino acids
    Molecular mass:
    58253 Da
    Quaternary structure:
    • Heterodimer of alpha and beta subunits.
    SequenceCaution:
    • Sequence=AAH33103.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA04643.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA09472.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PMPCA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PMPCA Gene

Selected DME Specific Peptides for PMPCA Gene

Q10713:
  • YPNIPLSSPLPGVPKP
  • RENTVGLHRFCP
  • GLESCSFLE
  • RLYLNVLNRHHWMYNATSYHHSYEDTGLLCIHASADPRQ
  • FATVDGQEKFETKVTTLDNGLRVASQNKFGQFCT
  • FSAGGPGKGM

Post-translational modifications for PMPCA Gene

  • Ubiquitination at Lys53, posLast=103103, posLast=232232, posLast=269269, and Lys488
  • Modification sites at PhosphoSitePlus

Other Protein References for PMPCA Gene

Domains & Families for PMPCA Gene

Gene Families for PMPCA Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q10713

UniProtKB/Swiss-Prot:

MPPA_HUMAN :
  • Belongs to the peptidase M16 family.
Family:
  • Belongs to the peptidase M16 family.
genes like me logo Genes that share domains with PMPCA: view

Function for PMPCA Gene

Molecular function for PMPCA Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
UniProtKB/Swiss-Prot Function:
Cleaves presequences (transit peptides) from mitochondrial protein precursors.

Enzyme Numbers (IUBMB) for PMPCA Gene

Phenotypes From GWAS Catalog for PMPCA Gene

Gene Ontology (GO) - Molecular Function for PMPCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004222 metalloendopeptidase activity TAS 10942759
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0008270 zinc ion binding IBA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PMPCA: view
genes like me logo Genes that share phenotypes with PMPCA: view

Human Phenotype Ontology for PMPCA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for PMPCA Gene

miRTarBase miRNAs that target PMPCA

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PMPCA
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PMPCA Gene

Localization for PMPCA Gene

Subcellular locations from UniProtKB/Swiss-Prot for PMPCA Gene

Mitochondrion matrix. Mitochondrion inner membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PMPCA gene
Compartment Confidence
extracellular 5
mitochondrion 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PMPCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0005739 mitochondrion IDA --
GO:0005743 mitochondrial inner membrane TAS 10942759
GO:0005759 mitochondrial matrix IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PMPCA: view

Pathways & Interactions for PMPCA Gene

genes like me logo Genes that share pathways with PMPCA: view

Pathways by source for PMPCA Gene

1 BioSystems pathway for PMPCA Gene
2 Reactome pathways for PMPCA Gene

Gene Ontology (GO) - Biological Process for PMPCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis TAS 10942759
GO:0006627 protein processing involved in protein targeting to mitochondrion IMP 25808372
GO:0006851 mitochondrial calcium ion transport TAS --
genes like me logo Genes that share ontologies with PMPCA: view

No data available for SIGNOR curated interactions for PMPCA Gene

Drugs & Compounds for PMPCA Gene

(1) Drugs for PMPCA Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zinc Approved Pharma 2359
genes like me logo Genes that share compounds with PMPCA: view

Transcripts for PMPCA Gene

Unigene Clusters for PMPCA Gene

Peptidase (mitochondrial processing) alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PMPCA
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PMPCA Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c · 8d · 8e ^ 9a · 9b · 9c · 9d · 9e ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^
SP1: - - - - - - -
SP2: - - -
SP3: - - - - - - -
SP4: - -
SP5:
SP6: -
SP7: - - -
SP8: - - - -
SP9: - - - -
SP10: -
SP11: - - - - -
SP12:
SP13:
SP14: - -

ExUns: 15a · 15b · 15c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for PMPCA Gene

GeneLoc Exon Structure for
PMPCA
ECgene alternative splicing isoforms for
PMPCA

Expression for PMPCA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PMPCA Gene

Protein differential expression in normal tissues from HIPED for PMPCA Gene

This gene is overexpressed in Lymph node (8.5) and Heart (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PMPCA Gene



Protein tissue co-expression partners for PMPCA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PMPCA Gene:

PMPCA

SOURCE GeneReport for Unigene cluster for PMPCA Gene:

Hs.495471

mRNA Expression by UniProt/SwissProt for PMPCA Gene:

Q10713-MPPA_HUMAN
Tissue specificity: Ubiquitously expressed with highest expression in fetal tissues and adult brain, cerebellum and cerebellar vermis.

Evidence on tissue expression from TISSUES for PMPCA Gene

  • Nervous system(4.7)
  • Intestine(4.6)
  • Kidney(4.6)
  • Bone marrow(4.3)
  • Skin(2.5)
  • Liver(2)
  • Lung(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PMPCA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • eye
  • head
Thorax:
  • lung
  • rib
  • rib cage
Abdomen:
  • intestine
  • large intestine
  • small intestine
Pelvis:
  • pelvis
Limb:
  • lower limb
General:
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with PMPCA: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PMPCA Gene

Orthologs for PMPCA Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PMPCA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PMPCA 34 33
  • 93.99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PMPCA 34 33
  • 86.16 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pmpca 33
  • 86.13 (n)
dog
(Canis familiaris)
Mammalia PMPCA 34 33
  • 85.7 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pmpca 16 34 33
  • 85.56 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PMPCA 34
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PMPCA 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves PMPCA 34 33
  • 73.37 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PMPCA 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pmpca 33
  • 75.48 (n)
Str.221 33
zebrafish
(Danio rerio)
Actinopterygii pmpca 33 34
  • 71.79 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6618 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008086 33
  • 58.12 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8728 33 34
  • 57.34 (n)
worm
(Caenorhabditis elegans)
Secernentea mppa-1 33 34
  • 46.79 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MAS2 33 34 36
  • 48.46 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E11573g 33
  • 48.02 (n)
rice
(Oryza sativa)
Liliopsida Os01g0966300 33
  • 45.18 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 64 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU06270 33
  • 51.65 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mas2 33
  • 44.15 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1704 33
Species where no ortholog for PMPCA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PMPCA Gene

ENSEMBL:
Gene Tree for PMPCA (if available)
TreeFam:
Gene Tree for PMPCA (if available)

Paralogs for PMPCA Gene

Paralogs for PMPCA Gene

(1) SIMAP similar genes for PMPCA Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for PMPCA Gene

genes like me logo Genes that share paralogs with PMPCA: view

Variants for PMPCA Gene

Sequence variations from dbSNP and Humsavar for PMPCA Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs746549806 Pathogenic, Spinocerebellar ataxia, autosomal recessive, 2 (SCAR2) [MIM:213200] 136,417,083(+) CCGGC(A/G)TGGGC reference, missense
rs869025292 Pathogenic, Spinocerebellar ataxia, autosomal recessive, 2 (SCAR2) [MIM:213200] 136,412,502(+) CAATT(C/T)AGGAT upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs869025293 Pathogenic, Spinocerebellar ataxia, autosomal recessive, 2 (SCAR2) [MIM:213200] 136,423,229(+) AGGAC(A/G)GGCGC downstream-variant-500B, reference, missense
VAR_076239 Spinocerebellar ataxia, autosomal recessive, 2 (SCAR2) [MIM:213200]
rs1057519454 Pathogenic 136,410,732(+) GTTCG(C/T)GGCTG upstream-variant-2KB, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for PMPCA Gene

Variant ID Type Subtype PubMed ID
esv2676242 CNV deletion 23128226
esv2759720 CNV loss 17122850
nsv469918 CNV loss 18288195
nsv509333 CNV insertion 20534489
nsv615963 CNV loss 21841781
nsv6766 CNV insertion 18451855
nsv825173 CNV gain 20364138
nsv825174 CNV gain 20364138
nsv831760 CNV loss 17160897
nsv951202 CNV deletion 24416366

Variation tolerance for PMPCA Gene

Residual Variation Intolerance Score: 19.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.65; 31.53% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PMPCA Gene

Human Gene Mutation Database (HGMD)
PMPCA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PMPCA

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PMPCA Gene

Disorders for PMPCA Gene

MalaCards: The human disease database

(11) MalaCards diseases for PMPCA Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia, autosomal recessive 2
  • autosomal recessive spinocerebellar ataxia 2
normal pressure hydrocephalus
  • low pressure hydrocephalus
3-methylglutaconic aciduria, type iii
  • optic atrophy plus syndrome
optic atrophy 3 with cataract
  • optic atrophy plus syndrome
optic atrophy plus syndrome
  • optic atrophy
- elite association - COSMIC cancer census association via MalaCards
Search PMPCA in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MPPA_HUMAN
  • Spinocerebellar ataxia, autosomal recessive, 2 (SCAR2) [MIM:213200]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR2 is characterized by onset of impaired motor development and ataxic gait in early childhood. Additional features often include loss of fine motor skills, dysarthria, nystagmus, cerebellar signs, and delayed cognitive development with intellectual disability. {ECO:0000269 PubMed:25808372, ECO:0000269 PubMed:26657514}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PMPCA

Genetic Association Database (GAD)
PMPCA
Human Genome Epidemiology (HuGE) Navigator
PMPCA
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PMPCA
genes like me logo Genes that share disorders with PMPCA: view

No data available for Genatlas for PMPCA Gene

Publications for PMPCA Gene

  1. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 8590280) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4 60
  2. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 7788527) Nagase T … Kotani H (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4 60
  3. Autosomal recessive cerebellar ataxia caused by a homozygous mutation in PMPCA. (PMID: 26657514) Choquet K … Tétreault M (Brain : a journal of neurology 2016) 3 4 60
  4. PMPCA mutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia. (PMID: 25808372) Jobling RK … Yoon G (Brain : a journal of neurology 2015) 3 4 60
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60

Products for PMPCA Gene

Sources for PMPCA Gene

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