Gene Gene information from NCBI Gene database.
Entrez ID 139411
Gene name Patched domain containing 1
Gene symbol PTCHD1
Synonyms (NCBI Gene)
AUTSX4CXDELp22.11DELXP22.11SLC65C1
Chromosome X
Chromosome location Xp22.11
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 in
SNPs SNP information provided by dbSNP.
15
SNP ID Visualize variation Clinical significance Consequence
rs150186077 T>C Conflicting-interpretations-of-pathogenicity, likely-benign Synonymous variant, coding sequence variant
rs797044922 TGTTG>GAA Pathogenic Frameshift variant, coding sequence variant
rs878854360 C>- Risk-factor Frameshift variant, coding sequence variant
rs878854361 C>- Risk-factor Frameshift variant, coding sequence variant
rs879255587 ->A Risk-factor Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
424
miRTarBase ID miRNA Experiments Reference
MIRT021976 hsa-miR-128-3p Microarray 17612493
MIRT627811 hsa-miR-511-3p HITS-CLIP 23313552
MIRT608834 hsa-miR-4455 HITS-CLIP 23313552
MIRT608833 hsa-miR-3650 HITS-CLIP 23313552
MIRT627810 hsa-miR-4796-5p HITS-CLIP 23313552
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
24
GO ID Ontology Definition Evidence Reference
GO:0005886 Component Plasma membrane IBA
GO:0005886 Component Plasma membrane IDA 20844286
GO:0005886 Component Plasma membrane IEA
GO:0007154 Process Cell communication IEA
GO:0007224 Process Smoothened signaling pathway IDA 20844286
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300828 26392 ENSG00000165186
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q96NR3
Protein name Patched domain-containing protein 1
Protein 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. Can bind cholesterol
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02460 Patched 49 851 Patched family Family
Tissue specificity 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. {ECO:0000269|PubMed:20844286}.
Sequence
MLRQVLHRGLRTCFSRLGHFIASHPVFFASAPVLISILLGASFSRYQVEESVEHLLAPQH
SLAKIERNLVNSLFPVNRSKHRLYSDLQTPGRYGRVIVTSFQKANMLDQHHTDLILKLHA
AVTKIQVPRPGFNYTFAHICILNNDKTCIVDDIVHVLEELKNARATNRTNFAITYPITHL
KDGRAVYNGHQLGGVTVHSKDRVKSAEAIQLTYYLQSINSLNDMVAERWESSFCDTVRLF
QKSNSKVKMYPYTSSSLREDFQKTSRVSERYLVTSLILVVTMAILCCSMQDCVRSKPWLG
LLGLVTISLATLTAAGIINLTGGKYNSTFLGVPFVMLGHGLYGTFEMLSSWRKTREDQHV
KERTAAVYADSMLSFSLTTAMYLVTFGIGASPFTNIEAARIFCCNSCIAIFFNYLYVLSF
YGSSLVFTGYIENNYQHSIFCRKVPKPEALQEKPAWYRFLLTARFSEDTAEGEEANTYES
HLLVCFLKRYYCDWITNTYVKPFVVLFYLIYISFALMGYLQVSEGSDLSNIVATATQTIE
YTTAQQKYFSNYSPVIGFYIYESIEYWNTSVQEDVLEYTKGFVRISWFESYLNYLRKLNV
STGLPKKNFTDMLRNSFLKAPQFSHFQEDIIFSKKYNDEVDVVASRMFLVAKTMETNREE
LYDLLETLRRLSVTSKVKFIVFNPSFVYMDRYASSLGAPLHNSCISALFLLFFSAFLVAD
SLINVWITLTVVSVEFGVIGFMTLWKVELDCISVLCLIYGINYTIDNCAPMLSTFVLGKD
FTRTKWVKNALEVHGVAILQSYLCYIVGLIPLAAVPSNLTCTLFRCLFLIAFVTFFHCFA
ILPVILTFLPP
SKKKRKEKKNPENREEIECVEMVDIDSTRVVDQITTV
Sequence length 888
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
23
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autism spectrum disorder Likely pathogenic rs1922524280 RCV001252599
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autism, susceptibility to, X-linked 4 Likely pathogenic; Pathogenic rs751692491, rs2518766952, rs2518767420, rs2518766477, rs1555912102 RCV001650488
RCV002286475
RCV003227586
RCV003236647
RCV004594827
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability Likely pathogenic rs1569130365 RCV001374406
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Non-syndromic X-linked intellectual disability Likely pathogenic rs1922892999 RCV001265487
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal brain morphology Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
2-3 toe syndactyly Syndactyly Of The Toes HPO_DG
★☆☆☆☆
Found in Text Mining only
Attention Deficit Disorder Attention Deficit Hyperactivity Disorder BEFREE 27007844
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder BEFREE 27007844, 31515500
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Autism Spectrum Disorder Autism Pubtator 18252227, 25782667, 31540669, 36635662, 38007613, 38275824 Associate
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autism Spectrum Disorders Autism Spectrum Disorder BEFREE 18252227, 20844286, 21439084, 22228009, 25131214, 25782667, 27007844, 28416808, 31515500, 31540669
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders Autism Spectrum Disorder CTD_human_DG 18252227, 20844286
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autistic behavior Autism BEFREE 25131214
★☆☆☆☆
Found in Text Mining only
Autistic behavior Autism HPO_DG
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism Pubtator 20531469, 21439084, 31540669, 36635662, 38007613 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations