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Gene

PTCHD1

patched domain containing 1

Summary

Cytogenetic location
Xp22.11
Coordinates
Chromosome X: 23,334,849–23,404,374 (GRCh38)
Exons
3 exons across 69.5 kb
Protein
888 amino acids
Also known as
SLC65C1, FLJ30296
MANE Select transcript
ENST00000379361.5NM_173495.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Autism Spectrum Disorder

    • Autism, susceptibility to (single-gene forms)

      Single-gene contributions to autism, including variants in NLGN3, NLGN4X, PTCHD1, SHANK2, TBR1 and CHD8.

      • 3 GenCC submitters rate it definitive or strong

  • Epilepsy (Full Panel)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong

Broader groupings

How PTCHD1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where PTCHD1 sits. PTCHD1 and 6 genes near it on chromosome X, from 22,869,612 to 23,869,611.Chromosome XXp22.11p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2823 Mb23.2 Mb23.4 Mb23.6 Mb23.8 MbDDX53: 22,999,960–23,003,589, forward strandDDX53PTCHD1: 23,334,849–23,404,374, forward strandPTCHD1PRDX4: 23,664,262–23,700,980, forward strandPRDX4ACOT9: 23,699,396–23,766,475, reverse strandACOT9SAT1: 23,783,171–23,786,210, forward strandSAT1: 23,783,278–23,783,367, forward strandAPOO: 23,833,348–23,908,070, reverse strandAPOODiagram of PTCHD1: 3 exons on the forward strand of chromosome XExon 1: 1 known disease-causing siteExon 2: 2 known disease-causing sitesExon 3: 5 known disease-causing sitesExon 1: 23,334,849–23,335,226, 378 basesExon 2: 23,379,591–23,380,251, 661 basesExon 3: 23,392,531–23,404,374, 11,844 bases1235′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 12.9 kb of the gene's 69.5 kb; 2,667 of those bases code for the protein.

How a genome test reads PTCHD1

8

positions in PTCHD1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 69.5 kb of PTCHD1, introns included, not only the 12.9 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PTCHD1 gene: patched domain containing 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/ptchd1

Vancouver

Dante Labs. PTCHD1 gene: patched domain containing 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ptchd1

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