Is PTCHD1 p.Val643= (c.1929G>A) pathogenic?

PTCHD1 p.Val643= (c.1929G>A) is classified Likely benign in PTCHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-05). Very rare (popmax 0.00112%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PTCHD1 p.Val643= (c.1929G>A)?

PTCHD1 p.Val643= (c.1929G>A) is associated with Inborn genetic diseases (ClinVar).

How common is PTCHD1 p.Val643= (c.1929G>A) in the general population?

PTCHD1 p.Val643= (c.1929G>A) is very rare (popmax 0.00112%, nfe) (gnomAD).

PTCHD1 p.Val643=

c.1929G>A · rs1922890939 · VCV1782819

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00112%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4	GERP 0.82, phastCons 1
Overall
CADD	7.203	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00112% European (non-Finnish) · 10/893,823 alleles

Filtering AF 0.000566% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000412%

Overall 0.000827% 10/1,209,884 alleles · very rare exomes 10/1,096,366 · genomes 0/113,518 · joint denominator

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.Val643=
Coding: c.1929G>A
MANE Select: NM_173495
dbSNP: rs1922890939
Type: single nucleotide variant
Location: chrX:23393447 (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.Val643Ala Uncertain significance ★ ⚠ same residue
PTCHD1 p.Val643Glu 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

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-val643 (accessed [today's date]).

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