PTCHD1

Chr XXLR

patched domain containing 1

Also known as: AUTSX4, CXDELp22.11, DELXP22.11, SLC65C1

NCBI Gene: 139411ENSG00000165186UniProt: Q96NR3OMIM: 300828

This gene encodes a membrane protein with a patched domain that is required for the development and function of the thalamic reticular nucleus, which is critical for thalamocortical transmission, sleep rhythms, sensorimotor processing and attention. Mutations cause X-linked intellectual disability and autism spectrum disorder. The gene shows X-linked recessive inheritance and is highly constrained against loss-of-function variants (pLI 0.98, LOEUF 0.28).

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismXLRLOEUF 0.281 OMIM phenotype
Clinical Summary— PTCHD1
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Gene-Disease Validity (ClinGen)
X-linked complex neurodevelopmental disorder · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.28LOEUF
pLI 0.982
Z-score 3.56
OE 0.06 (0.02–0.28)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.00Z-score
OE missense 0.70 (0.63–0.77)
238 obs / 342.3 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.06 (0.02–0.28)
0≤0.351.4
Missense OE0.70 (0.63–0.77)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 1 / 16.7Missense obs/exp: 238 / 342.3Syn Z: -0.23

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PTCHD1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Targeting the PTCHD1-hippo axis by rhPTH(1-34) restores contact inhibition and suppresses hyperproliferation in psoriatic keratinocytes.
Guo J et al.·Eur J Pharmacol
2026
The PTCHD1 protein: A prominent actor in brain function and in neurodevelopmental disorders.
Ung DC et al.·Neurosci Biobehav Rev
2025
Autism-Associated PTCHD1 Missense Variants Bind to the SNARE-Associated Protein SNAPIN but Exhibit Impaired Subcellular Trafficking.
Pastore SF et al.·Biol Psychiatry Glob Open Sci
2025Open Access
Corrigendum: PTCHD1 gene mutation/deletion: the cognitive-behavioral phenotyping of four case reports.
Montanaro FAM et al.·Front Psychiatry
2024Open AccessCase report
Nonsynonymous Mutations in Intellectual Disability and Autism Spectrum Disorder Gene PTCHD1 Disrupt N-Glycosylation and Reduce Protein Stability.
Xie CTY et al.·Cells
2024Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients