Is PTCH2 p.Arg754= (c.2262C>T) pathogenic?

PTCH2 p.Arg754= (c.2262C>T) is classified Likely benign in PTCH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-04). Ultra-rare (popmax 0.0158%, nfe); Associated with nevoid basal cell carcinoma syndrome.

What condition is associated with PTCH2 p.Arg754= (c.2262C>T)?

PTCH2 p.Arg754= (c.2262C>T) is associated with nevoid basal cell carcinoma syndrome (ClinVar).

How common is PTCH2 p.Arg754= (c.2262C>T) in the general population?

PTCH2 p.Arg754= (c.2262C>T) is ultra-rare (popmax 0.0158%, nfe) (gnomAD).

PTCH2 p.Arg754=

c.2262C>T · rs368434333 · VCV1105254

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0158%, nfe)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.6	GERP -3.8
Overall
CADD	7.388	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0158% European (non-Finnish) · 186/1,180,022 alleles

Filtering AF 0.0138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0132%

Overall 0.0124% 200/1,613,980 alleles · ultra-rare exomes 193/1,461,802 · genomes 7/152,178 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0158%	6,344
Remaining individualsnot grpmax-eligible	0.0064%	15,619
South Asian	0.00549%	18,216
African / African-American	0.004%	24,970
Admixed American	0.00167%	60,008
Finnishnot grpmax-eligible	0.00156%	64,024

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: PTCH2
Protein: p.Arg754=
Coding: c.2262C>T
MANE Select: NM_003738
dbSNP: rs368434333
Type: single nucleotide variant
Location: chr1:44827511 (GRCh38)
Gene constraint: LOEUF 0.895 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25
Residue 754: the 'extracellular domain 2 (ecd2)' 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.Arg754Cys Uncertain significance ★★ ⚠ same residue
PTCH2 p.Arg754His Uncertain significance ★★ ⚠ same residue
PTCH2 p.Arg754Ser 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

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-arg754 (accessed [today's date]).

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