Is CD36 p.Lys472fs (c.1416_*1del) pathogenic?

CD36 p.Lys472fs (c.14161del) is classified Conflicting classifications of pathogenicity in CD36 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-01-12). Rare (popmax 0.149%, amr); Associated with platelet-type bleeding disorder 10.

What condition is associated with CD36 p.Lys472fs (c.1416_*1del)?

CD36 p.Lys472fs (c.1416_*1del) is associated with platelet-type bleeding disorder 10 (ClinVar).

How common is CD36 p.Lys472fs (c.1416_*1del) in the general population?

CD36 p.Lys472fs (c.1416_*1del) is rare (popmax 0.149%, amr) (gnomAD).

CD36 p.Lys472fs

c.1416_*1del · rs771061715 · VCV692066

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.149%, amr)

Conditions

platelet-type bleeding disorder 10

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (14 of 15, 9 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -5.7	GERP -4
Overall
CADD	27.4	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 0.149% Admixed American · 89/59,778 alleles

Filtering AF 0.124% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.00926% 149/1,609,544 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.149%	672
African / African-American	0.0629%	1,591
East Asian	0.00672%	14,880
Remaining individualsnot grpmax-eligible	0.00481%	20,773
South Asian	0.0033%	30,306
European (non-Finnish)	0.00034%	294,206

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.Lys472fs
Coding: c.1416_*1del
MANE Select: NM_001001548
dbSNP: rs771061715
Type: Microsatellite
Location: chr7:80674138 (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 472: a cross-link site; the 'interaction with ptk2, pxn and lyn' region

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

Disease context

platelet-type bleeding disorder 10 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD36 p.Thr111fs Pathogenic/Likely pathogenic ★★ same condition
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.Gln262fs Pathogenic/Likely pathogenic ★★ same condition
CD36 p.Ile317fs Likely pathogenic ★★ same condition
CD36 p.Ile399fs Pathogenic/Likely pathogenic ★★ same condition
CD36 p.Ile410_Ile413del Pathogenic/Likely pathogenic ★★ 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-lys472fs (accessed [today's date]).

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