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

Gene ID: 442213, updated on 3-Apr-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 integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
6p12.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (47856673..48111197, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (47698467..47952968, complement)
105.20220307 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)

Genotypes

General gene information

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Markers

Homology

Clone Names

  • FLJ41841

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
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_2023_10

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

Gene LinkOut

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

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