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    PRTFDC1 phosphoribosyl transferase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 56952, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PRTFDC1provided by HGNC
    Official Full Name
    phosphoribosyl transferase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:23333
    See related
    Ensembl:ENSG00000099256 MIM:610751; AllianceGenome:HGNC:23333
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HHGP
    Summary
    Enables protein homodimerization activity. Predicted to be involved in purine ribonucleoside salvage. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 14.5), adrenal (RPKM 9.7) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRTFDC1 in Genome Data Viewer
    Location:
    10p12.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (24848614..24952606, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (24866903..24970863, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (25137543..25241535, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 21 Neighboring gene coenzyme Q10B pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2224 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:25012349-25013259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2228 Neighboring gene uncharacterized LOC105376456 Neighboring gene MPRA-validated peak910 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:25051766-25052318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3160 Neighboring gene NFE2L2 motif-containing MPRA enhancer 245 Neighboring gene RN7SK pseudogene 241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2229 Neighboring gene threonine synthase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2230 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:25305216-25305978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3162 Neighboring gene enkurin, TRPC channel interacting protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:25348855-25350054 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:25350646-25351845 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:25356859-25358058 Neighboring gene NANOG hESC enhancer GRCh37_chr10:25394727-25395330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2233 Neighboring gene long intergenic non-protein coding RNA 1516 Neighboring gene GPR158 antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. rs12411980 single-nucleotide polymorphism related to PRTFDC1 expression is significantly associated with phantom tooth pain. Araida J, et al. Mol Pain, 2024 Jan-Dec. PMID 39093623, Free PMC Article
    2. PRTFDC1, a possible tumor-suppressor gene, is frequently silenced in oral squamous-cell carcinomas by aberrant promoter hypermethylation. Suzuki E, et al. Oncogene, 2007 Dec 13. PMID 17599052
    3. Structural and functional studies of the human phosphoribosyltransferase domain containing protein 1. Welin M, et al. FEBS J, 2010 Dec. PMID 21054786
    4. PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse. Keebaugh AC, et al. PLoS One, 2011. PMID 21818316, Free PMC Article
    5. Genomic predictors of combat stress vulnerability and resilience in U.S. Marines: A genome-wide association study across multiple ancestries implicates PRTFDC1 as a potential PTSD gene. Nievergelt CM, et al. Psychoneuroendocrinology, 2015 Jan. PMID 25456346

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. rs12411980 single-nucleotide polymorphism related to PRTFDC1 expression is significantly associated with phantom tooth pain.
      Title: rs12411980 single-nucleotide polymorphism related to PRTFDC1 expression is significantly associated with phantom tooth pain.
    2. We found evidence for PRTFDC1 as a potential novel PTSD gene, a finding that awaits further replication.
      Title: Genomic predictors of combat stress vulnerability and resilience in U.S. Marines: A genome-wide association study across multiple ancestries implicates PRTFDC1 as a potential PTSD gene.
    3. These results demonstrate that PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse.
      Title: PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse.
    4. The PRTFDC1 structure has been determined at 1.7 A resolution with bound GMP. The overall structure and GMP binding mode are very similar to that observed for HPRT.
      Title: Structural and functional studies of the human phosphoribosyltransferase domain containing protein 1.
    5. epigenetic silencing of PRTFDC1 by hypermethylation of the CpG island leads to a loss of PRTFDC1 function, which might be involved in squamous cell oral carcinogenesis.
      Title: PRTFDC1, a possible tumor-suppressor gene, is frequently silenced in oral squamous-cell carcinomas by aberrant promoter hypermethylation.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Genomic predictors of combat stress vulnerability and resilience in U.S. Marines: A genome-wide association study across multiple ancestries implicates PRTFDC1 as a potential PTSD gene.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11888

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables hypoxanthine phosphoribosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in GMP catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in guanine salvage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in purine ribonucleoside salvage IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    phosphoribosyltransferase domain-containing protein 1
    NP_001269715.1
    NP_064585.1

    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.

    mRNA and Protein(s)

    1. NM_001282786.2 → NP_001269715.1  phosphoribosyltransferase domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001269715.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK021950, AK294130, AK309614, BQ003226
      Consensus CDS
      CCDS60506.1
      UniProtKB/Swiss-Prot
      Q9NRG1
      Related
      ENSP00000365558.1, ENST00000376378.5
      Conserved Domains (1) summary
      cl00309
      Location:7 → 184
      PRTases_typeI; Phosphoribosyl transferase (PRT)-type I domain

    2. NM_020200.7 → NP_064585.1  phosphoribosyltransferase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_064585.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK021950, AK309614, BQ003226
      Consensus CDS
      CCDS7145.1
      UniProtKB/Swiss-Prot
      B7Z1Z3, Q53HA7, Q59EL9, Q5VV18, Q5VV20, Q9NRG1
      Related
      ENSP00000318602.5, ENST00000320152.11
      Conserved Domains (1) summary
      cl00309
      Location:7 → 224
      PRTases_typeI; Phosphoribosyl transferase (PRT)-type I domain

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      24848614..24952606 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      24866903..24970863 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NRG1.1 GenPept UniProtKB/Swiss-Prot:Q9NRG1

    Gene LinkOut

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

    Other Literature Sources
    Chemical Information
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