Is CD82 p.Leu105Phe (c.313C>T) pathogenic?

CD82 p.Leu105Phe (c.313C>T) is classified Uncertain significance in CD82 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-21). AlphaMissense: likely benign (0.1869); Very rare (popmax 0.00167%, amr).

How common is CD82 p.Leu105Phe (c.313C>T) in the general population?

CD82 p.Leu105Phe (c.313C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about CD82 p.Leu105Phe (c.313C>T)?

AlphaMissense predicts likely benign (score 0.1869) — an in-silico prediction, not a clinical call.

CD82 p.Leu105Phe

c.313C>T · VCV3998351

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1869 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1869	likely benign
REVEL	0.424	indeterminate
SaProt	LLR -8.76	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.029	GERP 0.21, phastCons 0.001
Regional constraint	o/e 0.98	unconstrained · MANE · 24 kb · p 0.71 · regional, not allelic
Overall
CADD	10.79	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,012 alleles

Overall 0.000657% 1/152,220 alleles · very rare

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.Leu105Phe
Coding: c.313C>T
MANE Select: NM_002231
Type: single nucleotide variant
Location: chr11:44605406 (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.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
CD82 p.Asn17Ser 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-leu105phe (accessed [today's date]).

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