Is CD36 p.Pro90Ser (c.268C>T) pathogenic?

CD36 p.Pro90Ser (c.268C>T) is classified Conflicting classifications of pathogenicity in CD36 (ClinVar, Conflicting submitters, 9 submitters; last evaluated 2026-01-05). AlphaMissense: likely pathogenic (0.9661); Low-frequency (popmax 2.98%, eas); Associated with inherited bleeding disorder, platelet-type.

What condition is associated with CD36 p.Pro90Ser (c.268C>T)?

CD36 p.Pro90Ser (c.268C>T) is associated with inherited bleeding disorder, platelet-type, platelet-type bleeding disorder 10 (ClinVar).

How common is CD36 p.Pro90Ser (c.268C>T) in the general population?

CD36 p.Pro90Ser (c.268C>T) is low-frequency (popmax 2.98%, eas) (gnomAD).

What do computational predictors say about CD36 p.Pro90Ser (c.268C>T)?

AlphaMissense predicts likely pathogenic (score 0.9661) — an in-silico prediction, not a clinical call.

CD36 p.Pro90Ser

c.268C>T · rs75326924 · VCV13535

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 9 submitters

AlphaMissense

likely pathogenic

0.9661 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.98%, eas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

inherited bleeding disorder, platelet-type

Computational evidence

Protein change
AlphaMissense	0.9661	likely pathogenic · top 7% in CD36
REVEL	0.944	strongly pathogenic-leaning
SaProt	LLR -11.46	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.49 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 1.47	unconstrained · MANE · 27 kb · p 5.1e-29 · regional, not allelic
Overall
CADD	26.7	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 2.98% East Asian · 1,336/44,774 alleles

Filtering AF 2.85% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.8%

Overall 0.0837% 1,351/1,613,448 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	2.98%	34
Remaining individualsnot grpmax-eligible	0.0176%	5,680
South Asian	0.00329%	30,354
Admixed American	0.00167%	59,960

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.Pro90Ser
Coding: c.268C>T
MANE Select: NM_001001548
dbSNP: rs75326924
Type: single nucleotide variant
Location: chr7:80656687 (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 90: a UniProt-annotated variant site (in pg4d; type i; degradation in the cytoplasm due to defects in maturation); a β-strand

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

Disease context

inherited bleeding disorder, platelet-type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: platelet-type bleeding disorder 10

Similar variants

CD36 c.1254+1G>A Likely pathogenic ★★ same condition
CD36 c.430-2A>G Likely pathogenic ★★ same condition
CD36 p.Cys243Ter Pathogenic ★★ same condition
CD36 p.Leu381Ter Pathogenic/Likely pathogenic ★★ same condition
CD36 p.Tyr62Ter Likely pathogenic ★★ same condition
CD36 c.-27C>T Uncertain significance ★★ same condition
CD36 p.Ala427Ser Uncertain significance ★★ ⚠ same condition
CD36 p.Arg292Ile Uncertain significance ★★ ⚠ 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-pro90ser (accessed [today's date]).

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