CD209 p.Thr174=
c.522T>C · rs551425556 · VCV2649177
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00874%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | |
| Overall | ||
| CADD | 0.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00874%
African / African-American · 6/68,626 alleles
Filtering AF
0.00373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00256%
Overall
0.00139%
22/1,584,448 alleles · very rare
exomes 15/1,451,498 · genomes 7/132,950 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00874% | 11,438 |
| East Asian | 0.00227% | 44,092 |
| Finnishnot grpmax-eligible | 0.00187% | 53,478 |
| European (non-Finnish) | 0.00119% | 83,791 |
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.Thr174=
- Coding
- c.522T>C
- MANE Select
- NM_021155
- dbSNP
- rs551425556
- Type
- single nucleotide variant
- Location
- chr19:7745744 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 16 PDB
- Residue 174
- the '7 x approximate tandem repeats' region
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-thr174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown