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    PTCHD4 patched domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 442213, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PTCHD4provided by HGNC
    Official Full Name
    patched domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:21345
    See related
    Ensembl:ENSG00000244694 MIM:616908; AllianceGenome:HGNC:21345
    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
    PTCH53; C6orf138; dJ402H5.2
    Summary
    Predicted to be active in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See PTCHD4 in Genome Data Viewer
    Location:
    6p12.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (47856673..48111197, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (47698467..47952968, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (47824409..48078933, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene opsin 5 Neighboring gene RNA, U1 small nuclear 105, pseudogene Neighboring gene uncharacterized LOC107986601 Neighboring gene Sharpr-MPRA regulatory region 3755 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:48078458-48079657 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 4 Neighboring gene RBMX pseudogene 1

    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
    • 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 PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. Chung JH, et al. J Biol Chem, 2014 Nov 21. PMID 25296753, Free PMC Article
    2. Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium. Guan W, et al. Circ Cardiovasc Genet, 2014 Jun. PMID 24823311, Free PMC Article
    3. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
    4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. Bailey SD, et al. Diabetes Care, 2010 Oct. PMID 20628086, Free PMC Article
    5. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Talmud PJ, et al. Am J Hum Genet, 2009 Nov. PMID 19913121, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data indicate that tumor suppressor p53 can suppress canonical Hedgehog signaling via induction of patched domain containing 4 (PTCH53), a PTCH1 homolog.
      Title: A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling.
    2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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 plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    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)

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ41841

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    patched domain-containing protein 4
    Names
    p53-regulated patched protein
    patched domain-containing protein C6orf138

    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_001013732.4 → NP_001013754.3  patched domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001013754.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AK299301, AL161622, AL353138, KF458157
      UniProtKB/Swiss-Prot
      A0A0A7EN49, B0QZ29, B2RPC0, B4DRK3, B4DTR9, Q5T884, Q6ZW05
      Conserved Domains (2) summary
      pfam02460
      Location:148 → 812
      Patched; Patched family
      cl21543
      Location:257 → 408
      MMPL; MMPL family

    2. NM_001384253.1 → NP_001371182.1  patched domain-containing protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL121973, AL161622, AL353138, KF458157
      Consensus CDS
      CCDS93929.1
      Related
      ENSP00000341914.5, ENST00000339488.9
      Conserved Domains (1) summary
      cl25655
      Location:145 → 809
      Patched; Patched family

    3. NM_001410910.1 → NP_001397839.1  patched domain-containing protein 4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL121973, AL161622, AL353138
      Consensus CDS
      CCDS93930.1
      UniProtKB/TrEMBL
      H0Y3Q6
      Related
      ENSP00000381722.3, ENST00000398738.3

    4. NM_207499.2 → NP_997382.2  patched domain-containing protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a different segment for its 3' end, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus when it is compared to isoform 1.
      Source sequence(s)
      AK123835, AK299301, AL161622
      UniProtKB/TrEMBL
      A0A7P0TAD5
      Conserved Domains (1) summary
      cl21543
      Location:257 → 307
      MMPL; MMPL family

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      47856673..48111197 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514639.3 → XP_011512941.1  patched domain-containing protein 4 isoform X4

      UniProtKB/Swiss-Prot
      Q6ZW05
      Conserved Domains (2) summary
      pfam02460
      Location:1 → 559
      Patched; Patched family
      cl21543
      Location:4 → 155
      MMPL; MMPL family

    2. XM_047418830.1 → XP_047274786.1  patched domain-containing protein 4 isoform X5

    3. XM_017010892.2 → XP_016866381.1  patched domain-containing protein 4 isoform X2

      Conserved Domains (2) summary
      pfam02460
      Location:138 → 867
      Patched; Patched family
      cl21543
      Location:312 → 463
      MMPL; MMPL family

    4. XM_017010891.2 → XP_016866380.1  patched domain-containing protein 4 isoform X1

    5. XM_017010895.2 → XP_016866384.1  patched domain-containing protein 4 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      47698467..47952968 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355517.1 → XP_054211492.1  patched domain-containing protein 4 isoform X4

    2. XM_054355515.1 → XP_054211490.1  patched domain-containing protein 4 isoform X2

    3. XM_054355514.1 → XP_054211489.1  patched domain-containing protein 4 isoform X1

    4. XM_054355516.1 → XP_054211491.1  patched domain-containing protein 4 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZW05.3 GenPept UniProtKB/Swiss-Prot:Q6ZW05

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