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

    Gene ID: 139411, updated on 14-Nov-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
    mouse all
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    Genomic context

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    See PTCHD1 in Genome Data Viewer
    Location:
    Xp22.11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (23334396..23404374)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (22917921..22987936)
    RS_2024_09 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 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. CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction. Farley KO, et al. HGG Adv, 2024 Jan 11. PMID 38007613, Free PMC Article
    2. 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
    3. 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
    4. 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
    5. 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

    See all (17) 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
    		not available
    Autism, susceptibility to, X-linked 4
    MedGen: C0795888 OMIM: 300830 GeneReviews: Not available
    		not available

    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)

    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

    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
    located_in dendritic spine IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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_2024_08

    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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