CD9 p.Leu76=
c.228G>A · rs114003206 · VCV736570
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
East Asian · 543/43,392 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.0365%
577/1,579,618 alleles · low-frequency
exomes 522/1,427,410 · genomes 55/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 0.0244% | 4,091 |
| Admixed American | 0.00356% | 28,122 |
| South Asian | 0.00231% | 43,358 |
| European (non-Finnish) | 0.00129% | 77,755 |
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
- CD9
- Protein
- p.Leu76=
- Coding
- c.228G>A
- MANE Select
- NM_001769
- dbSNP
- rs114003206
- Type
- single nucleotide variant
- Location
- chr12:6232684 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 88.38 · 5 PDB
- Residue 76
- an α-helix
Similar variants
- CD9 c.447+8G>A Benign ★★ same type
- CD9 p.Asn51Thr Uncertain significance ★ ⚠ same type
- CD9 p.Glu103Gln Uncertain significance ★ ⚠ same type
- CD9 p.Gly210Ala Uncertain significance ★ ⚠ same type
- CD9 p.Gly80Arg Uncertain significance ★ ⚠ same type
- CD9 p.Leu96Phe Uncertain significance ★ ⚠ same type
- CD9 p.Lys186Glu Uncertain significance ★ ⚠ same type
- CD9 p.Met227Leu Uncertain significance ★ ⚠ 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/cd9-p-leu76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown