CD209 p.Ile294=
c.882C>A · rs759862642 · VCV750352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.045 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.8 | GERP -2.1 |
| Overall | ||
| CADD | 0.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,088 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000342%
5/1,461,864 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,363 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- CD209
- Protein
- p.Ile294=
- Coding
- c.882C>A
- MANE Select
- NM_021155
- dbSNP
- rs759862642
- Type
- single nucleotide variant
- Location
- chr19:7744959 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 16 PDB
- Residue 294
- the c-type lectin domain; a disulfide bond; an α-helix
Similar variants
- CD209 p.Gln189Leu Uncertain significance ★★ ⚠ same type
- CD209 p.Glu214Asp Uncertain significance ★★ ⚠ same type
- CD209 p.Ala357= Benign ★★ same type
- CD209 p.Ala395= Benign ★★ same type
- CD209 p.Asp331= Benign ★★ same type
- CD209 p.Ala132Ser Uncertain significance ★ ⚠ same type
- CD209 p.Ala202Val Uncertain significance ★ ⚠ same type
- CD209 p.Asp75Gly 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/cd209-p-ile294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown