PTCHD4
protein-codingpatched domain containing 4
Gene summary
Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C6orf138
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~254.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PTCHD4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001384253.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 131 | 2 | 133 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 132 | 3 | 0 | 135 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001371182.1 | 4 | MANE Select | |
| Ensembl | ENSP00000341914.5 | 4 | MANE Select | |
| RefSeq | NP_001013754.3 | 3 | Standard | |
| RefSeq | NP_001397839.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
Cellular Component
- cellular_component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339488
- Coding exons
- 3
- Length
- 190662
- Individuals with no LoFs
- 125565
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125593
- p
- 0.000111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0727 | 468 | 464 | 1.01 | 0.0000239 | 5569 |
| Missense (PolyPhen) | 246 | 249.16 | 0.98731 | 3089 | ||
| Synonymous | -1.64 | 224 | 195 | 1.15 | 0.0000105 | 1689 |
| Loss of Function | 2.82 | 11 | 26.7 | 0.412 | 0.00000151 | 307 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00012 | 0.00011 | rare |
| Finnish | 0.000096 | 0.000092 | rare |
| European (Non-Finnish) | 0.000090 | 0.000088 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Could act as a repressor of canonical hedgehog signaling by antagonizing the effects of SMO, as suggested by down- regulation of hedgehog target genes, including GLI1, PTCH1, and PTCH2 in PTCHD4-expressing cells. {ECO:0000269|PubMed:25296753}.;
Intolerance Scores
- RVIS EVS
- -0.71
- RVIS percentile EVS
- 14.71
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |