Is CD82 p.Pro265Leu (c.794C>T) pathogenic?

CD82 p.Pro265Leu (c.794C>T) is classified Uncertain significance in CD82 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-07). AlphaMissense: ambiguous (0.3945); Ultra-rare (popmax 0.0198%, nfe).

How common is CD82 p.Pro265Leu (c.794C>T) in the general population?

CD82 p.Pro265Leu (c.794C>T) is ultra-rare (popmax 0.0198%, nfe) (gnomAD).

What do computational predictors say about CD82 p.Pro265Leu (c.794C>T)?

AlphaMissense predicts ambiguous (score 0.3945) — an in-silico prediction, not a clinical call.

CD82 p.Pro265Leu

c.794C>T · rs201671713 · VCV3998348

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3945 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0198%, nfe)

Computational evidence

Protein change
AlphaMissense	0.3945	ambiguous
REVEL	0.306	indeterminate
SaProt	LLR -12.44	damaging
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.33 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.4	GERP 1.2, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 24 kb · p 0.71 · regional, not allelic
Overall
CADD	27.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0198% European (non-Finnish) · 233/1,179,674 alleles

Filtering AF 0.0177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0168%

Overall 0.0156% 252/1,613,390 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0198%	5,063
Remaining individualsnot grpmax-eligible	0.0144%	6,942
African / African-American	0.00669%	14,954
Admixed American	0.00667%	14,996
East Asian	0.00223%	44,812

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: CD82
Protein: p.Pro265Leu
Coding: c.794C>T
MANE Select: NM_002231
dbSNP: rs201671713
Type: single nucleotide variant
Location: chr11:44619116 (GRCh38)
Gene constraint: LOEUF 1.221 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.31 · 1 PDB

Full CD82 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD82 p.Pro265Ser Uncertain significance ★ ⚠ same residue
CD82 p.Gly233= Benign ★★ same type
CD82 p.Leu248= Benign ★★ same type
CD82 p.Val62= Benign ★★ same type
CD82 p.Ala195Val Uncertain significance ★ ⚠ same type
CD82 p.Arg254Trp Uncertain significance ★ ⚠ same type
CD82 p.Arg53Ser Uncertain significance ★ ⚠ same type
CD82 p.Asn109Ser Uncertain significance ★ ⚠ same type

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/cd82-p-pro265leu (accessed [today's date]).

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