Is CD36 p.Cys313Ter (c.939C>A) pathogenic?

CD36 p.Cys313Ter (c.939C>A) is classified Likely pathogenic in CD36 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-12-29). Rare (popmax 0.148%, mid); Associated with CD36-related disorder.

What condition is associated with CD36 p.Cys313Ter (c.939C>A)?

CD36 p.Cys313Ter (c.939C>A) is associated with CD36-related disorder (ClinVar).

How common is CD36 p.Cys313Ter (c.939C>A) in the general population?

CD36 p.Cys313Ter (c.939C>A) is rare (popmax 0.148%, mid) (gnomAD).

CD36 p.Cys313Ter

c.939C>A · VCV3353009

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.148%, mid)

Conditions

CD36-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 10 of 15
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
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.148% Middle Eastern · 9/6,076 alleles

Filtering AF 0.0772% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0577%

Overall 0.00242% 39/1,612,578 alleles · rare exomes 38/1,460,484 · genomes 1/152,094 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.148%	675
South Asian	0.00659%	15,178
Remaining individualsnot grpmax-eligible	0.00641%	15,606
Admixed American	0.00333%	29,988
European (non-Finnish)	0.00153%	65,497

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: CD36
Protein: p.Cys313Ter
Coding: c.939C>A
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

Disease context

CD36-related disorder

Similar variants

CD36 p.Cys313Ser Uncertain significance ★ ⚠ same residue
CD36 p.Cys313Trp Uncertain significance ★ ⚠ same residue
CD36 p.Cys313Tyr Uncertain significance ★ ⚠ same residue
CD36 p.Arg292Ile Uncertain significance ★★ ⚠ same condition
CD36 c.1255-1G>C Likely pathogenic ★ same condition
CD36 c.429+2T>C Conflicting classifications of pathogenicity ★ same condition
CD36 c.609+1G>A Conflicting classifications of pathogenicity ★ same condition
CD36 p.Arg386Trp Conflicting classifications of pathogenicity ★ ⚠ 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/cd36-p-cys313ter (accessed [today's date]).

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