CFAP418 p.Lys58=
c.174A>G · rs754956516 · VCV1681143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
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 1.7, phastCons 1 |
| Overall | ||
| CADD | 3.277 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/90,794 alleles
Filtering AF
0.0128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00138%
20/1,453,428 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,044 |
| Admixed American | 0.00334% | 29,963 |
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
- CFAP418
- Protein
- p.Lys58=
- Coding
- c.174A>G
- MANE Select
- NM_177965
- dbSNP
- rs754956516
- Type
- single nucleotide variant
- Location
- chr8:95263756 (GRCh38)
- Gene constraint
- LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
- Residue 58
- the 'required for interaction with fam161a' region
Similar variants
- CFAP418 p.Lys58Gln Uncertain significance ★ ⚠ same residue
- CFAP418 p.Lys58Glu Uncertain significance ★ ⚠ same residue
- CFAP418 p.Lys58fs Likely pathogenic same residue
- CFAP418 p.Arg177Trp Pathogenic/Likely pathogenic ★★ same type
- CFAP418 p.Trp147Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP418 p.Trp185Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP418 c.*408G>A Uncertain significance ★★ same type
- CFAP418 c.*965C>G 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/cfap418-p-lys58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown