Is PTCH2 p.Pro255= (c.765T>C) pathogenic?

PTCH2 p.Pro255= (c.765T>C) is classified Likely benign in PTCH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-27). No allele count reported in gnomAD v4.1 (AN 1,576,550); Associated with nevoid basal cell carcinoma syndrome.

What condition is associated with PTCH2 p.Pro255= (c.765T>C)?

PTCH2 p.Pro255= (c.765T>C) is associated with nevoid basal cell carcinoma syndrome (ClinVar).

How common is PTCH2 p.Pro255= (c.765T>C) in the general population?

PTCH2 p.Pro255= (c.765T>C) is no allele count reported in gnomAD v4.1 (AN 1,576,550) (gnomAD).

PTCH2 p.Pro255=

c.765T>C · VCV3604600

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,576,550)

Conditions

nevoid basal cell carcinoma syndrome

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 -1.6	GERP -3.5
Overall
CADD	4.399	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,576,550). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PTCH2
Protein: p.Pro255=
Coding: c.765T>C
MANE Select: NM_003738
Type: single nucleotide variant
Location: chr1:44830896 (GRCh38)
Gene constraint: LOEUF 0.895 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25
Residue 255: the 'extracellular domain 1 (ecd1)' region

Full PTCH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nevoid basal cell carcinoma syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTCH2 p.Pro255Ala Uncertain significance ★★ ⚠ same residue
PTCH2 p.Pro255Arg Uncertain significance ★ ⚠ same residue
PTCH2 c.2976+2T>C Uncertain significance ★★ same condition
PTCH2 c.526-2A>G Uncertain significance ★★ same condition
PTCH2 c.618-6C>A Uncertain significance ★★ same condition
PTCH2 p.Ala1052Thr Uncertain significance ★★ ⚠ same condition
PTCH2 p.Ala1090Val Uncertain significance ★★ ⚠ same condition
PTCH2 p.Ala203Val 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/ptch2-p-pro255 (accessed [today's date]).

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