PTCHD1
patched domain containing 1
Basic information
Region (hg38): X:23334849-23404374
Links
Phenotypes
GenCC
Source:
- autism, susceptibility to, X-linked 4 (Strong), mode of inheritance: XL
- autism, susceptibility to, X-linked 4 (Definitive), mode of inheritance: XL
- autism, susceptibility to, X-linked 4 (Definitive), mode of inheritance: XL
- non-syndromic X-linked intellectual disability (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Autism susceptibility, X-linked 4 | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 18252227; 21091464; 25131214 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (156 variants)
- Inborn_genetic_diseases (102 variants)
- Autism,_susceptibility_to,_X-linked_4 (33 variants)
- not_specified (21 variants)
- PTCHD1-related_disorder (13 variants)
- Intellectual_disability (2 variants)
- Tatton-Brown-Rahman_overgrowth_syndrome (1 variants)
- Neurodevelopmental_disorder (1 variants)
- PTCHD1-related_neurodevelopmental_disorder (1 variants)
- PTCHD1-related_autism_and_intellectual_disability (1 variants)
- Autism_spectrum_disorder (1 variants)
- Abnormal_brain_morphology (1 variants)
- See_cases (1 variants)
- Rare_genetic_intellectual_disability (1 variants)
- Non-syndromic_X-linked_intellectual_disability (1 variants)
- Developmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCHD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173495.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 34 | 42 | ||||
| missense | 171 | 23 | 202 | |||
| nonsense | 8 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 11 | 23 | ||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 7 | 24 | 186 | 57 | 3 |
Highest pathogenic variant AF is 9.25771e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTCHD1 | protein_coding | protein_coding | ENST00000379361 | 3 | 70357 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.982 | 0.0178 | 125350 | 0 | 1 | 125351 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.00 | 238 | 342 | 0.695 | 0.0000258 | 5849 |
| Missense in Polyphen | 69 | 135.04 | 0.51096 | 2434 | ||
| Synonymous | -0.225 | 148 | 145 | 1.02 | 0.0000114 | 1794 |
| Loss of Function | 3.56 | 1 | 16.7 | 0.0599 | 0.00000112 | 336 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000524 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- 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. {ECO:0000250|UniProtKB:Q14B62}.;
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.0945
- rvis_EVS
- -1
- rvis_percentile_EVS
- 8.32
Haploinsufficiency Scores
- pHI
- 0.532
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.625
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.238
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptchd1
- Phenotype
- growth/size/body region phenotype; muscle phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype;
Gene ontology
- Biological process
- smoothened signaling pathway;thalamus development;social behavior;cognition
- Cellular component
- plasma membrane;integral component of membrane
- Molecular function
- molecular_function