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    PITRM1 pitrilysin metallopeptidase 1 [ Homo sapiens (human) ]

    Gene ID: 10531, updated on 17-Jun-2024

    Summary

    Official Symbol
    PITRM1provided by HGNC
    Official Full Name
    pitrilysin metallopeptidase 1provided by HGNC
    Primary source
    HGNC:HGNC:17663
    See related
    Ensembl:ENSG00000107959 MIM:618211; AllianceGenome:HGNC:17663
    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
    MP1; PreP; SCAR30
    Summary
    The protein encoded by this gene is an ATP-dependent metalloprotease that degrades post-cleavage mitochondrial transit peptides. The encoded protein binds zinc and can also degrade amyloid beta A4 protein, suggesting a possible role in Alzheimer's disease. [provided by RefSeq, Dec 2016]
    Annotation information
    Note: The official gene symbol PREP (prolyl endopeptidase) on GeneID: 5550 can be confused with the alias for presequence protease (PREP) on GeneID: 10531 whose official symbol is PITRM1 (pitrilysin metallopeptidase 1). [20 Jun 2018]
    Expression
    Ubiquitous expression in testis (RPKM 24.8), adrenal (RPKM 18.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PITRM1 in Genome Data Viewer
    Location:
    10p15.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (3137727..3172841, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (3138971..3174045, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (3179919..3215033, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene wiskott-Aldrich syndrome protein family member 1-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2070 Neighboring gene PFKP divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2905 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:3110992-3111172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3115641-3116142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3118349-3118913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3118914-3119477 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:3119931-3120866 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:3126799-3126967 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:3132863-3134062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3134597-3135394 Neighboring gene phosphofructokinase, platelet Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:3137343-3138542 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:3146075-3147274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:3171407-3171920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3178175-3178676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3178677-3179176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3183533-3184034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3184035-3184534 Neighboring gene small nucleolar RNA, C/D box 142 Neighboring gene PITRM1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:3215987-3216524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3256260-3256760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3256761-3257261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:3279001-3279500 Neighboring gene long intergenic non-protein coding RNA 2668 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:3290932-3292131 Neighboring gene mucin-5AC-like Neighboring gene ReSE screen-validated silencer GRCh37_chr10:3305040-3305205 Neighboring gene uncharacterized LOC124902537 Neighboring gene uncharacterized LOC107987146

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Spinocerebellar ataxia, autosomal recessive 30
    MedGen: C5543620 OMIM: 619405 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1104, MGC138192, MGC141929

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme activator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables metalloendopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables metalloendopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metalloendopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables metallopeptidase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in protein processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein targeting to mitochondrion TAS
    Traceable Author Statement
    more info
     
    involved_in proteolysis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    presequence protease, mitochondrial
    Names
    PreP peptidasome
    metalloprotease 1 (pitrilysin family)
    pitrilysin metalloproteinase 1
    NP_001229236.1
    NP_001229238.1
    NP_001334654.1
    NP_001334655.1
    NP_001334656.1
    NP_001334657.1
    NP_001334658.1
    NP_001334659.1
    NP_055704.2
    XP_047280401.1
    XP_047280402.1
    XP_054220465.1
    XP_054220466.1

    NCBI Reference Sequences (RefSeq)

    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_052908.1 RefSeqGene

      Range
      5060..40114
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001242307.2NP_001229236.1  presequence protease, mitochondrial isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF061243, AL451164, BC005025
      Consensus CDS
      CCDS55699.1
      UniProtKB/TrEMBL
      A0A7I2YQT2
      Related
      ENSP00000370377.2, ENST00000380989.6
      Conserved Domains (4) summary
      COG1026
      Location:441010
      Cym1; Zn-dependent peptidase, M16 (insulinase) family [Posttranslational modification, protein turnover, chaperones]
      pfam00675
      Location:71177
      Peptidase_M16; Insulinase (Peptidase family M16)
      pfam05193
      Location:245432
      Peptidase_M16_C; Peptidase M16 inactive domain
      pfam08367
      Location:506750
      M16C_assoc; Peptidase M16C associated
    2. NM_001242309.1NP_001229238.1  presequence protease, mitochondrial isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at an alternate AUG and results an isoform (3) with a distinct N-terminus, compared to isoform 1. The encoded protein likely does not localize to the mitochondrion.
      Source sequence(s)
      AK002061, AK303406, AL451164, BC095422, DA331909
      Consensus CDS
      CCDS55700.1
      UniProtKB/TrEMBL
      B4DH07
      Related
      ENSP00000401201.2, ENST00000451104.6
      Conserved Domains (4) summary
      COG1026
      Location:20911
      Cym1; Zn-dependent peptidase, M16 (insulinase) family [Posttranslational modification, protein turnover, chaperones]
      pfam00675
      Location:39145
      Peptidase_M16; Insulinase (Peptidase family M16)
      pfam05193
      Location:213400
      Peptidase_M16_C; Peptidase M16 inactive domain
      pfam08367
      Location:474651
      M16C_assoc; Peptidase M16C associated
    3. NM_001347725.2NP_001334654.1  presequence protease, mitochondrial isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) encodes isoform 4.
      Source sequence(s)
      AL451164
      Consensus CDS
      CCDS91206.1
      UniProtKB/TrEMBL
      A0A7I2V397, A0A7I2YQT2
      Related
      ENSP00000503187.1, ENST00000678436.1
    4. NM_001347726.2NP_001334655.1  presequence protease, mitochondrial isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) encodes isoform 5, which likely does not localize to the mitochondrion.
      Source sequence(s)
      AL451164
    5. NM_001347727.2NP_001334656.1  presequence protease, mitochondrial isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) encodes isoform 6, which likely does not localize to the mitochondrion.
      Source sequence(s)
      AL451164
      Consensus CDS
      CCDS91205.1
      UniProtKB/TrEMBL
      A0A0A0MRX9, B4DRW8
      Related
      ENSP00000370382.2, ENST00000380994.6
    6. NM_001347728.2NP_001334657.1  presequence protease, mitochondrial isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) encodes isoform 7, which likely does not localize to the mitochondrion.
      Source sequence(s)
      AL451164
      UniProtKB/TrEMBL
      B3KN37
    7. NM_001347729.1NP_001334658.1  presequence protease, mitochondrial isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) encodes isoform 8, which likely does not localize to the mitochondrion.
      Source sequence(s)
      AL451164
      UniProtKB/TrEMBL
      A0A7I2YQT2
    8. NM_001347730.1NP_001334659.1  presequence protease, mitochondrial isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) encodes isoform 9, which likely does not localize to the mitochondrion.
      Source sequence(s)
      AL451164
      UniProtKB/TrEMBL
      A0A7I2YQT2
    9. NM_014889.4NP_055704.2  presequence protease, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_055704.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AL451164, BC005025, BC113369
      Consensus CDS
      CCDS59208.1
      UniProtKB/Swiss-Prot
      B3KMJ6, B4E0J8, C9JSL2, E7ES23, O95204, Q2M2G6, Q4VBR1, Q5JRW7, Q5JRX3, Q7L5Z7, Q9BSI6, Q9BVJ5, Q9UPP8
      UniProtKB/TrEMBL
      A0A7I2YQT2
      Related
      ENSP00000224949.4, ENST00000224949.9
      Conserved Domains (4) summary
      COG1026
      Location:441009
      Cym1; Zn-dependent peptidase, M16 (insulinase) family [Posttranslational modification, protein turnover, chaperones]
      pfam00675
      Location:71177
      Peptidase_M16; Insulinase (Peptidase family M16)
      pfam05193
      Location:245432
      Peptidase_M16_C; Peptidase M16 inactive domain
      pfam08367
      Location:506749
      M16C_assoc; Peptidase M16C associated

    RNA

    1. NR_144638.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL451164
      Related
      ENST00000677001.1
    2. NR_144639.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL451164
    3. NR_144640.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL451164
    4. NR_144641.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL451164

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      3137727..3172841 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424446.1XP_047280402.1  presequence protease, mitochondrial isoform X2

      UniProtKB/TrEMBL
      H0Y4F7
      Related
      ENSP00000391526.2, ENST00000430362.2
    2. XM_047424445.1XP_047280401.1  presequence protease, mitochondrial isoform X1

      UniProtKB/TrEMBL
      H0Y4F7
      Related
      ENSP00000503630.1, ENST00000677817.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      3138971..3174045 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364491.1XP_054220466.1  presequence protease, mitochondrial isoform X4

      UniProtKB/TrEMBL
      H0Y4F7
    2. XM_054364490.1XP_054220465.1  presequence protease, mitochondrial isoform X3

      UniProtKB/TrEMBL
      H0Y4F7

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_014968.1: Suppressed sequence

      Description
      NM_014968.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.