CFAP58 p.Glu238=
c.714A>G · VCV3388081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0472%, 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 2 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 6.942 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0472%
South Asian · 43/91,064 alleles
Filtering AF
0.036%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0321%
Overall
0.0175%
282/1,613,526 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0472% | 2,118 |
| European (non-Finnish) | 0.0187% | 5,338 |
| Middle Eastern | 0.0165% | 6,076 |
| African / African-American | 0.00935% | 10,694 |
| Admixed American | 0.00834% | 11,986 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,615 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,596 |
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
- CFAP58
- Protein
- p.Glu238=
- Coding
- c.714A>G
- MANE Select
- NM_001008723
- Type
- single nucleotide variant
- Location
- chr10:104365930 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.87 · 1 PDB
Similar variants
- CFAP58 p.Thr783Met Uncertain significance ★★ ⚠ same type
- CFAP58 p.Arg698Ter Pathogenic ★ same type
- CFAP58 p.Gln454Ter Likely pathogenic ★ same type
- CFAP58 c.2039+3A>G Uncertain significance ★ same type
- CFAP58 p.Ala102Thr Uncertain significance ★ ⚠ same type
- CFAP58 p.Ala177Pro Uncertain significance ★ ⚠ same type
- CFAP58 p.Ala311Thr Uncertain significance ★ ⚠ same type
- CFAP58 p.Ala311Val 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/cfap58-p-glu238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown