Is CD36 p.Cys313Trp (c.939C>G) pathogenic?

CD36 p.Cys313Trp (c.939C>G) is classified Uncertain significance in CD36 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-28). AlphaMissense: likely pathogenic (0.9925); Absent from gnomAD v4.1.

How common is CD36 p.Cys313Trp (c.939C>G) in the general population?

CD36 p.Cys313Trp (c.939C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD36 p.Cys313Trp (c.939C>G)?

AlphaMissense predicts likely pathogenic (score 0.9925) — an in-silico prediction, not a clinical call.

CD36 p.Cys313Trp

c.939C>G · VCV3998241

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9925 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9925	likely pathogenic · top 1% in CD36
REVEL	0.873	moderately pathogenic-leaning
SaProt	LLR -15.18	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.001	GERP 0.38, phastCons 0.78
Regional constraint	o/e 1.47	unconstrained · MANE · 27 kb · p 5.1e-29 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD36
Protein: p.Cys313Trp
Coding: c.939C>G
MANE Select: NM_001001548
Type: single nucleotide variant
Location: chr7:80671097 (GRCh38)
Gene constraint: LOEUF 1.953 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 94.14 · 1 PDB
Residue 313: a disulfide bond

Full CD36 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD36 p.Cys313Ter Likely pathogenic ★ same residue
CD36 p.Cys313Ser Uncertain significance ★ ⚠ same residue
CD36 p.Cys313Tyr Uncertain significance ★ ⚠ same residue
CD36 c.1254+1G>A Likely pathogenic ★★ same type
CD36 c.430-2A>G Likely pathogenic ★★ same type
CD36 p.Cys243Ter Pathogenic ★★ same type
CD36 p.Leu381Ter Pathogenic/Likely pathogenic ★★ same type
CD36 p.Tyr62Ter Likely pathogenic ★★ 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/cd36-p-cys313trp (accessed [today's date]).

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