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PTCHD1 patched domain containing 1 [ Homo sapiens (human) ]

Gene ID: 139411, updated on 5-Mar-2024

Summary

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Official Symbol
PTCHD1provided by HGNC
Official Full Name
patched domain containing 1provided by HGNC
Primary source
HGNC:HGNC:26392
See related
Ensembl:ENSG00000165186 MIM:300828; AllianceGenome:HGNC:26392
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
AUTSX4; DELXP22.11; CXDELp22.11
Summary
This gene encodes a membrane protein with a patched domain. The encoded protein is similar to Drosophila proteins which act as receptors for the morphogen sonic hedgehog. Deletions in this gene, which is located on the X chromosome, are associated with intellectual disability and autism (PMID: 21091464, PMID: 20844286). [provided by RefSeq, Aug 2011]
Expression
Biased expression in brain (RPKM 1.9), endometrium (RPKM 0.9) and 12 other tissues See more
Orthologs
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Genomic context

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Location:
Xp22.11
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (23334396..23404374)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (22917921..22987936)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (23352966..23422491)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PTCHD1 antisense RNA (head to head) Neighboring gene ReSE screen-validated silencer GRCh37_chrX:23111444-23111682 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:23155798-23156034 Neighboring gene FAM3C pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:23256953-23257600 Neighboring gene PDCL2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20702 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:23362831-23363330 Neighboring gene HIKESHI pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:23523568-23524107 Neighboring gene Sharpr-MPRA regulatory region 9198 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:23526452-23526963 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:23677931-23678536 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:23678537-23679142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:23682591-23683125 Neighboring gene Sharpr-MPRA regulatory region 11823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20704 Neighboring gene peroxiredoxin 4

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. Novel missense mutations in PTCHD1 alter its plasma membrane subcellular localization and cause intellectual disability and autism spectrum disorder. Halewa J, et al. Hum Mutat, 2021 Jul. PMID 33856728, Free PMC Article
  2. Synaptic Dysfunction in Human Neurons With Autism-Associated Deletions in PTCHD1-AS. Ross PJ, et al. Biol Psychiatry, 2020 Jan 15. PMID 31540669, Free PMC Article
  3. Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. Torrico B, et al. Eur J Hum Genet, 2015 Dec. PMID 25782667, Free PMC Article
  4. Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder. Chaudhry A, et al. Clin Genet, 2015 Sep. PMID 25131214
  5. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism. Filges I, et al. Clin Genet, 2011 Jan. PMID 21091464

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Nonsynonymous Mutations in Intellectual Disability and Autism Spectrum Disorder Gene PTCHD1 Disrupt N-Glycosylation and Reduce Protein Stability.
    Title: Nonsynonymous Mutations in Intellectual Disability and Autism Spectrum Disorder Gene PTCHD1 Disrupt N-Glycosylation and Reduce Protein Stability.
  2. CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction.
    Title: CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction.
  3. Novel missense mutations in PTCHD1 alter its plasma membrane subcellular localization and cause intellectual disability and autism spectrum disorder.
    Title: Novel missense mutations in PTCHD1 alter its plasma membrane subcellular localization and cause intellectual disability and autism spectrum disorder.
  4. Synaptic Dysfunction in Human Neurons With Autism-Associated Deletions in PTCHD1-AS.
    Title: Synaptic Dysfunction in Human Neurons With Autism-Associated Deletions in PTCHD1-AS.
  5. both common and rare PTCHD1 variants contribute to autism spectrum disorder.
    Title: Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability.
  6. Our findings suggest that hemizygous PTCHD1 loss of function causes an X-linked neurodevelopmental disorder with a strong propensity to autistic behaviors.
    Title: Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder.
  7. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism.
    Title: Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism.
  8. Systematic screen of PTCHD1 and its 5' flanking regions suggests that this locus is involved in ~1% of individuals with autism spectrum disorder and intellectual disability.
    Title: Disruption at the PTCHD1 Locus on Xp22.11 in Autism spectrum disorder and intellectual disability.
  9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Functional impact of global rare copy number variation in autism spectrum disorders.
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

Associated conditions

Description Tests
Autism spectrum disorder
MedGen: C1510586 GeneReviews: Not available
Compare labs
Autism, susceptibility to, X-linked 4
MedGen: C0795888 OMIM: 300830 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-02-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2018-02-28)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30296, MGC149798

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 chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cognition IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cognition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in excitatory chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in inhibitory chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in long-term memory IEA
Inferred from Electronic Annotation
more info
  
involved_in short-term memory IEA
Inferred from Electronic Annotation
more info
  
involved_in smoothened signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in social behavior ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in thalamus development ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
patched domain-containing protein 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.

Genomic

  1. NG_021300.1 RefSeqGene

    Range
    5001..66934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_173495.3 → NP_775766.2  patched domain-containing protein 1

    See identical proteins and their annotated locations for NP_775766.2

    Status: VALIDATED

    Source sequence(s)
    AC073910, BC121061, BX107899, DC351268, DC365753
    Consensus CDS
    CCDS35215.2
    UniProtKB/Swiss-Prot
    B4DQH0, Q0IJ60, Q6P6B8, Q96NR3
    UniProtKB/TrEMBL
    X5DNX9
    Related
    ENSP00000368666.4, ENST00000379361.5
    Conserved Domains (1) summary
    cl25655
    Location:105 → 851
    Patched; Patched 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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    23334396..23404374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545449.4 → XP_011543751.1  patched domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011543751.1

    UniProtKB/Swiss-Prot
    B4DQH0, Q0IJ60, Q6P6B8, Q96NR3
    UniProtKB/TrEMBL
    X5DNX9
    Conserved Domains (1) summary
    cl25655
    Location:105 → 851
    Patched; Patched family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    22917921..22987936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326481.1 → XP_054182456.1  patched domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DQH0, Q0IJ60, Q6P6B8, Q96NR3
    UniProtKB/TrEMBL
    X5DNX9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96NR3.2 GenPept UniProtKB/Swiss-Prot:Q96NR3

Gene LinkOut

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

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