CFAP99 p.Ala172Thr
c.514G>A · VCV3491507
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00594%, 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 -1.1 | GERP -4.3 |
| Regional constraint | o/e 1.08 | unconstrained · MANE · 36 kb · p 0.016 · regional, not allelic |
| Overall | ||
| CADD | 0.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00594%
European (non-Finnish) · 65/1,094,998 alleles
Filtering AF
0.00477%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00435%
Overall
0.00485%
69/1,423,604 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00594% | 16,846 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00434% | 23,026 |
| Admixed American | 0.00291% | 34,364 |
| Finnishnot grpmax-eligible | 0.00244% | 41,054 |
| Remaining individualsnot grpmax-eligible | 0.00181% | 55,138 |
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.Ala172Thr
- Coding
- c.514G>A
- MANE Select
- NM_001193282
- Type
- single nucleotide variant
- Location
- chr4:2445180 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.28
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-ala172thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown