Is PTCHD1 p.Val26= (c.78C>T) pathogenic?

PTCHD1 p.Val26= (c.78C>T) is classified Likely benign in PTCHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-12-03). Very rare (popmax 0.00701%, afr); Associated with Inborn genetic diseases.

What condition is associated with PTCHD1 p.Val26= (c.78C>T)?

PTCHD1 p.Val26= (c.78C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PTCHD1 p.Val26= (c.78C>T) in the general population?

PTCHD1 p.Val26= (c.78C>T) is very rare (popmax 0.00701%, afr) (gnomAD).

PTCHD1 p.Val26=

c.78C>T · rs776836458 · VCV1761117

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00701%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -0.17, phastCons 1
Overall
CADD	12.18	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00701% African / African-American · 4/57,027 alleles

Filtering AF 0.00238% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.0029% 35/1,206,118 alleles · very rare exomes 28/1,095,134 · genomes 7/110,984 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00701%	14,257
European (non-Finnish)	0.00336%	29,782
Remaining individualsnot grpmax-eligible	0.00211%	47,433

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PTCHD1
Protein: p.Val26=
Coding: c.78C>T
MANE Select: NM_173495
dbSNP: rs776836458
Type: single nucleotide variant
Location: chrX:23334953 (GRCh38)
Structure: AlphaFold pLDDT 84.14

Full PTCHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTCHD1 p.Val26Ile Uncertain significance ★ ⚠ same residue
PTCHD1 p.Ala314Thr Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Arg238Ser Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Asn818Ser Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Gly194Ser Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Ile153Thr Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Ile35Met Uncertain significance ★★ ⚠ same condition
PTCHD1 p.Leu17Val Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ptchd1-p-val26 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown