CFAP99 p.Val209Met
c.625G>A · rs777982448 · VCV3143767
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0153%, nfe)
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 -6.5 | GERP -4.3 |
| Regional constraint | o/e 1.08 | unconstrained · MANE · 36 kb · p 0.016 · regional, not allelic |
| Overall | ||
| CADD | 0.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0153%
European (non-Finnish) · 162/1,062,260 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0126%
Overall
0.0131%
179/1,364,262 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0153% | 6,557 |
| East Asian | 0.0147% | 6,782 |
| Remaining individualsnot grpmax-eligible | 0.00956% | 10,460 |
| African / African-American | 0.00904% | 11,059 |
| Finnishnot grpmax-eligible | 0.00259% | 38,684 |
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
- CFAP99
- Protein
- p.Val209Met
- Coding
- c.625G>A
- MANE Select
- NM_001193282
- dbSNP
- rs777982448
- Type
- single nucleotide variant
- Location
- chr4:2445291 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.28
- Residue 209
- the 'disordered' region
Similar variants
- CFAP99 p.Ala255Thr Uncertain significance ★ same type
- CFAP99 p.Ala307Thr Uncertain significance ★ same type
- CFAP99 p.Ala366Thr Uncertain significance ★ same type
- CFAP99 p.Ala369Gly Uncertain significance ★ same type
- CFAP99 p.Ala396Val Uncertain significance ★ same type
- CFAP99 p.Ala423Thr Uncertain significance ★ same type
- CFAP99 p.Ala428Thr Uncertain significance ★ same type
- CFAP99 p.Ala450Ser 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/cfap99-p-val209met (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown