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

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

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

RH48273 (e-PCR)
- UniSTS:79432

DXS8104 (e-PCR), detects polymorphism
- UniSTS:6562

RH46883 (e-PCR)
- UniSTS:54207

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
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

NG_021300.1 RefSeqGene

Range

5001..66934

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

23334396..23404374

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060947.1 Alternate T2T-CHM13v2.0

Range

22917921..22987936

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B4DQH0, Q0IJ60, Q6P6B8, Q96NR3

UniProtKB/TrEMBL

X5DNX9