Is CD36 c.609+1G>A pathogenic?

CD36 c.609+1G>A is classified Conflicting classifications of pathogenicity in CD36 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-07-01). Rare (popmax 0.214%, mid); Associated with CD36-related disorder.

What condition is associated with CD36 c.609+1G>A?

CD36 c.609+1G>A is associated with CD36-related disorder (ClinVar).

How common is CD36 c.609+1G>A in the general population?

CD36 c.609+1G>A is rare (popmax 0.214%, mid) (gnomAD).

CD36 c.609+1G>A

rs755124649 · VCV632010

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

Consequence

canonical splice-site (±1/±2)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.214%, mid)

Conditions

CD36-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	canonical splice-site (±1/±2)	predicted loss-of-function
Splicing
Splice region	donor +1	canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone
SpliceAI	Δ0.51	donor loss · deltas
Pangolin	Δ0.33	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 10	GERP 1.6, phastCons 1
Non-coding constraint	Z -3.42	1 kb window · o/e 1.27 · regional · uncalibrated
Overall
CADD	32.0	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 0.214% Middle Eastern · 13/6,074 alleles

Filtering AF 0.127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.1%

Overall 0.00503% 81/1,609,666 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.214%	467
Remaining individualsnot grpmax-eligible	0.0241%	4,156
Admixed American	0.0133%	7,496
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,570
European (non-Finnish)	0.00332%	30,161
South Asian	0.0033%	30,326
East Asian	0.00223%	44,776
African / African-American	0.00134%	74,784

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
Coding: c.609+1G>A
MANE Select: NM_001001548
dbSNP: rs755124649
Type: single nucleotide variant
Location: chr7:80663170 (GRCh38)
Gene constraint: LOEUF 1.953 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 94.14 · 1 PDB

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

Disease context

CD36-related disorder

Similar variants

CD36 p.Arg292Ile Uncertain significance ★★ ⚠ same condition
CD36 c.1255-1G>C Likely pathogenic ★ same condition
CD36 p.Cys313Ter Likely pathogenic ★ same condition
CD36 c.429+2T>C Conflicting classifications of pathogenicity ★ same condition
CD36 p.Arg386Trp Conflicting classifications of pathogenicity ★ ⚠ same condition
CD36 p.Leu360Ter Conflicting classifications of pathogenicity ★ same condition
CD36 c.1126-7T>G Uncertain significance same condition
CD36 c.1200-8T>C Likely benign 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-c-609-plus-1g-a (accessed [today's date]).

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