Is CD82 p.Pro265Ser (c.793C>T) pathogenic?

CD82 p.Pro265Ser (c.793C>T) is classified Uncertain significance in CD82 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-01). AlphaMissense: ambiguous (0.3863); Rare (popmax 0.112%, afr).

How common is CD82 p.Pro265Ser (c.793C>T) in the general population?

CD82 p.Pro265Ser (c.793C>T) is rare (popmax 0.112%, afr) (gnomAD).

What do computational predictors say about CD82 p.Pro265Ser (c.793C>T)?

AlphaMissense predicts ambiguous (score 0.3863) — an in-silico prediction, not a clinical call.

CD82 p.Pro265Ser

c.793C>T · rs147912305 · VCV2388678

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3863 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.112%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.3863	ambiguous
REVEL	0.211	benign-leaning
SaProt	LLR -9.86	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
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	26.3	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 0.112% African / African-American · 84/74,822 alleles

Filtering AF 0.0929% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0857%

Overall 0.00558% 90/1,613,446 alleles · rare exomes 37/1,461,558 · genomes 53/151,888 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.112%	891
Admixed American	0.00834%	11,993
European (non-Finnish)	8.48e-05%	1,179,720

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.Pro265Ser
Coding: c.793C>T
MANE Select: NM_002231
dbSNP: rs147912305
Type: single nucleotide variant
Location: chr11:44619115 (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.Pro265Leu 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-pro265ser (accessed [today's date]).

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