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PTCHD1 Gene(Protein Coding)

Patched Domain Containing 1

GCID:
GC0XP023352
GIFtS:
44
Genes Participants
UDN Logo

Aliases for PTCHD1 Gene

Aliases for PTCHD1 Gene

  • Patched Domain Containing 1 2 3 5
  • Patched Domain-Containing Protein 1 3
  • PTCHD1 Isoform 3
  • AUTSX4 3

External Ids for PTCHD1 Gene

Previous GeneCards Identifiers for PTCHD1 Gene

  • GC0XP023112
  • GC0XP023262
  • GC0XP021094

Summaries for PTCHD1 Gene

Entrez Gene Summary for PTCHD1 Gene

  • 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]

GeneCards Summary for PTCHD1 Gene

PTCHD1 (Patched Domain Containing 1) is a Protein Coding gene. Diseases associated with PTCHD1 include Autism X-Linked 4 and Autism Spectrum Disorder. Gene Ontology (GO) annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is PTCHD4.

UniProtKB/Swiss-Prot for PTCHD1 Gene

  • Required for the development and function of the thalamic reticular nucleus (TRN), a part of the thalamus that is critical for thalamocortical transmission, generation of sleep rhythms, sensorimotor processing and attention.

Additional gene information for PTCHD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTCHD1 Gene

Genomics for PTCHD1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PTCHD1 Gene

Promoters and enhancers for PTCHD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XI023333 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 550.8 +0.3 299 1.1 SP3 GLIS1 ZBTB26 EZH2 PTCHD1 LOC100217367
GH0XI023334 Enhancer 0.4 ENCODE 550.8 -0.5 -517 0.2 ZNF213 GLIS1 EZH2 PTCHD1 PIR57627
GH0XI023666 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 9.1 +333.6 333640 2.7 SMAD1 ZNF133 ARID4B SIN3A DMAP1 ZNF2 BRCA1 ZNF48 YY1 KLF7 PRDX4 PTCHD1 ACOT9
GH0XI023372 Enhancer 0.7 FANTOM5 ENCODE 16.4 +38.9 38930 1.1 HIC1 JUND ZBTB21 ZBTB48 ATF2 PTCHD1 PIR56820 GC0XP023538
GH0XI023699 Enhancer 1 Ensembl ENCODE 5.5 +365.8 365800 0.8 HDAC1 TCF12 GATA2 E2F8 ATF7 NCOA1 ZEB2 ZNF148 MBD2 NFIC PTCHD1 PRDX4 ACOT9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PTCHD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PTCHD1 gene promoter:

Genomic Locations for PTCHD1 Gene

Genomic Locations for PTCHD1 Gene
chrX:23,334,016-23,404,372
(GRCh38/hg38)
Size:
70,357 bases
Orientation:
Plus strand
chrX:23,352,133-23,422,489
(GRCh37/hg19)

Genomic View for PTCHD1 Gene

Genes around PTCHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCHD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PTCHD1 Gene

Proteins for PTCHD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PTCHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96NR3-PTHD1_HUMAN
    Recommended name:
    Patched domain-containing protein 1
    Protein Accession:
    Q96NR3
    Secondary Accessions:
    • B4DQH0
    • Q0IJ60
    • Q6P6B8

    Protein attributes for PTCHD1 Gene

    Size:
    888 amino acids
    Molecular mass:
    101341 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PTCHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTCHD1 Gene

Post-translational modifications for PTCHD1 Gene

  • Glycosylation at isoforms=77, isoforms=2, 3133, isoforms=2, 3167, Asn319, isoforms=2, 3326, isoforms=2568, Asn599, isoforms=2608, Asn762, and Asn818
  • Modification sites at PhosphoSitePlus

Other Protein References for PTCHD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PTCHD1 Gene

Domains & Families for PTCHD1 Gene

Gene Families for PTCHD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PTCHD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PTCHD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96NR3

UniProtKB/Swiss-Prot:

PTHD1_HUMAN :
  • Belongs to the patched family.
Family:
  • Belongs to the patched family.
genes like me logo Genes that share domains with PTCHD1: view

Function for PTCHD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PTCHD1 Gene

UniProtKB/Swiss-Prot Function:
Required for the development and function of the thalamic reticular nucleus (TRN), a part of the thalamus that is critical for thalamocortical transmission, generation of sleep rhythms, sensorimotor processing and attention.

Phenotypes From GWAS Catalog for PTCHD1 Gene

Gene Ontology (GO) - Molecular Function for PTCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with PTCHD1: view
genes like me logo Genes that share phenotypes with PTCHD1: view

Human Phenotype Ontology for PTCHD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTCHD1 Gene

MGI Knock Outs for PTCHD1:

Animal Model Products

miRNA for PTCHD1 Gene

miRTarBase miRNAs that target PTCHD1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PTCHD1 Gene

Localization for PTCHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCHD1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTCHD1 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for PTCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA,IDA 20844286
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PTCHD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PTCHD1 Gene

Pathways & Interactions for PTCHD1 Gene

SuperPathways for PTCHD1 Gene

PathCards logo More details on SuperPathways for PTCHD1
No Data Available

Interacting Proteins for PTCHD1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 7)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000368666%0d%0a9606.ENSP00000376570%0d%0a9606.ENSP00000344260%0d%0a9606.ENSP00000329654%0d%0a9606.ENSP00000313983%0d%0a9606.ENSP00000279386%0d%0a
Selected Interacting proteins: Q96NR3-PTHD1_HUMAN ENSP00000368666 for PTCHD1 Gene via IID STRING

Gene Ontology (GO) - Biological Process for PTCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007224 smoothened signaling pathway IDA 20844286
GO:0021794 thalamus development IEA,ISS --
GO:0035176 social behavior IEA,ISS --
GO:0050890 cognition IEA,IMP 20844286
genes like me logo Genes that share ontologies with PTCHD1: view

No data available for Pathways by source and SIGNOR curated interactions for PTCHD1 Gene

Drugs & Compounds for PTCHD1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PTCHD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PTCHD1 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PTCHD1 Gene

Patched domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTCHD1 Gene

No ASD Table

Relevant External Links for PTCHD1 Gene

GeneLoc Exon Structure for
PTCHD1
ECgene alternative splicing isoforms for
PTCHD1

Expression for PTCHD1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTCHD1 Gene

mRNA expression in normal human tissues for PTCHD1 Gene
mRNA expression by GTEx for PTCHD1 GenemRNA expression by BioGPS for PTCHD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PTCHD1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x8.2), Brain - Cerebellum (x7.9), and Colon - Sigmoid (x4.9).

NURSA nuclear receptor signaling pathways regulating expression of PTCHD1 Gene:

PTCHD1

SOURCE GeneReport for Unigene cluster for PTCHD1 Gene:

Hs.319503

mRNA Expression by UniProt/SwissProt for PTCHD1 Gene:

Q96NR3-PTHD1_HUMAN
Tissue specificity: Widely expressed, including in various regions of the brain with highest expression in the gray and white cerebellum, followed by the cerebellar vermis and the pituitary gland.

Evidence on tissue expression from TISSUES for PTCHD1 Gene

  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCHD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
  • testicle
  • urinary bladder
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PTCHD1: view

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for PTCHD1 Gene

Orthologs for PTCHD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTCHD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PTCHD1 33 34
  • 97.42 (n)
dog
(Canis familiaris)
 Mammalia PTCHD1 33 34
  • 96.32 (n)
oppossum
(Monodelphis domestica)
 Mammalia PTCHD1 34
  • 95 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia PTCHD1 33 34
  • 94.78 (n)
mouse
(Mus musculus)
 Mammalia Ptchd1 33 16 34
  • 94.07 (n)
rat
(Rattus norvegicus)
 Mammalia Ptchd1 33
  • 94.03 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia PTCHD1 34
  • 86 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PTCHD1 33 34
  • 87.21 (n)
lizard
(Anolis carolinensis)
 Reptilia PTCHD1 34
  • 89 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia ptchd1 33
  • 77.93 (n)
zebrafish
(Danio rerio)
 Actinopterygii ptchd1 33 34
  • 68.36 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Ptr 34
  • 19 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea ptr-2 34
  • 22 (a)
 ManyToMany
ptr-10 34
  • 19 (a)
 ManyToMany
ptr-15 34
  • 19 (a)
 ManyToMany
ptr-19 34
  • 19 (a)
 ManyToMany
daf-6 34
  • 18 (a)
 ManyToMany
ptr-17 34
  • 18 (a)
 ManyToMany
ptr-9 34
  • 18 (a)
 ManyToMany
ptr-1 34
  • 17 (a)
 ManyToMany
ptr-20 34
  • 17 (a)
 ManyToMany
ptr-6 34
  • 17 (a)
 ManyToMany
ptr-16 34
  • 16 (a)
 ManyToMany
ptr-18 34
  • 16 (a)
 ManyToMany
ptr-21 34
  • 16 (a)
 ManyToMany
ptr-22 34
  • 16 (a)
 ManyToMany
ptr-5 34
  • 16 (a)
 ManyToMany
ptr-13 34
  • 15 (a)
 ManyToMany
ptr-14 34
  • 15 (a)
 ManyToMany
ptr-23 34
  • 15 (a)
 ManyToMany
ptr-3 34
  • 15 (a)
 ManyToMany
ptr-11 34
  • 14 (a)
 ManyToMany
ptr-12 34
  • 14 (a)
 ManyToMany
ptr-4 34
  • 14 (a)
 ManyToMany
ptr-8 34
  • 14 (a)
 ManyToMany
Species where no ortholog for PTCHD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PTCHD1 Gene

ENSEMBL:
Gene Tree for PTCHD1 (if available)
TreeFam:
Gene Tree for PTCHD1 (if available)

Paralogs for PTCHD1 Gene

Paralogs for PTCHD1 Gene

(2) SIMAP similar genes for PTCHD1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with PTCHD1: view

Variants for PTCHD1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PTCHD1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1060499615 uncertain-significance, Autism, susceptibility to, X-linked 4 23,380,146(+) G/A coding_sequence_variant, missense_variant
rs1060499778 likely-pathogenic, Abnormality of brain morphology 23,379,781(+) A/C coding_sequence_variant, missense_variant
rs797044922 pathogenic, Inborn genetic diseases 23,393,353(+) TGTTG/GAA coding_sequence_variant, frameshift
rs878854360 risk-factor, Autism, susceptibility to, X-linked 4 23,393,645(+) CC/C coding_sequence_variant, frameshift
rs878854361 risk-factor, Autism, susceptibility to, X-linked 4 23,392,961(+) CC/C coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for PTCHD1 Gene

Variant ID Type Subtype PubMed ID
esv3573649 CNV loss 25503493
nsv521962 CNV gain 19592680

Variation tolerance for PTCHD1 Gene

Residual Variation Intolerance Score: 5.18% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTCHD1 Gene

Human Gene Mutation Database (HGMD)
PTCHD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTCHD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTCHD1 Gene

Disorders for PTCHD1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PTCHD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
autism x-linked 4
  • autism, susceptibility to, x-linked 4
autism spectrum disorder
  • asd
pervasive developmental disorder
  • pervasive development disorder
autism
  • autistic disorder
x-linked non-specific intellectual disability
  • x-linked non-syndromic intellectual disability
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PTHD1_HUMAN
  • Autism, X-linked 4 (AUTSX4) [MIM:300830]: A complex multifactorial, pervasive developmental disorder characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism also manifest moderate mental retardation. {ECO:0000269 PubMed:20844286, ECO:0000269 PubMed:25131214, ECO:0000269 PubMed:25782667}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for PTCHD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PTCHD1: view

No data available for Genatlas for PTCHD1 Gene

Publications for PTCHD1 Gene

  1. Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder. (PMID: 25131214) Chaudhry A … Carter MT (Clinical genetics 2015) 3 4 58
  2. Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. (PMID: 25782667) Torrico B … Toma C (European journal of human genetics : EJHG 2015) 3 4 58
  3. Functional impact of global rare copy number variation in autism spectrum disorders. (PMID: 20531469) Pinto D … Betancur C (Nature 2010) 3 44 58
  4. Disruption at the PTCHD1 Locus on Xp22.11 in Autism spectrum disorder and intellectual disability. (PMID: 20844286) Noor A … Vincent JB (Science translational medicine 2010) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for PTCHD1 Gene

Sources for PTCHD1 Gene

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