CFAP99 p.Arg460Cys
c.1378C>T · rs961382746 · VCV2512441
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0412%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.134 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 1.08 | unconstrained · MANE · 36 kb · p 0.016 · regional, not allelic |
| Overall | ||
| CADD | 24.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0412%
Admixed American · 21/50,968 alleles
Filtering AF
0.0275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.00775%
119/1,535,540 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0412% | 2,427 |
| Remaining individualsnot grpmax-eligible | 0.0217% | 4,614 |
| Finnishnot grpmax-eligible | 0.00904% | 11,067 |
| European (non-Finnish) | 0.00663% | 15,089 |
| South Asian | 0.00357% | 28,015 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00349% | 28,640 |
| East Asian | 0.00244% | 40,920 |
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.Arg460Cys
- Coding
- c.1378C>T
- MANE Select
- NM_001193282
- dbSNP
- rs961382746
- Type
- single nucleotide variant
- Location
- chr4:2459181 (GRCh38)
- Gene constraint
- LOEUF 1.203 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.28
Similar variants
- CFAP99 p.Arg460His Uncertain significance ★ same residue
- 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
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-arg460cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown