FRMD7 p.Ser558=
c.1674C>T · rs369003419 · VCV1165233
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0402%, afr)
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 -1.5 | GERP -3 |
| Overall | ||
| CADD | 0.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0402%
African / African-American · 23/57,256 alleles
Filtering AF
0.0274%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0232%
Overall
0.00289%
35/1,209,291 alleles · ultra-rare
exomes 20/1,097,318 · genomes 15/111,973 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0402% | 2,489 |
| South Asian | 0.0106% | 9,465 |
| East Asian | 0.00296% | 33,755 |
| Admixed American | 0.00218% | 45,784 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,600 |
| European (non-Finnish) | 0.000335% | 298,138 |
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
- FRMD7
- Protein
- p.Ser558=
- Coding
- c.1674C>T
- MANE Select
- NM_194277
- dbSNP
- rs369003419
- Type
- single nucleotide variant
- Location
- chrX:132078343 (GRCh38)
- Structure
- AlphaFold pLDDT 62.31
Similar variants
- FRMD7 p.Ser558Arg Uncertain significance ★ ⚠ same residue
- FRMD7 c.906-2A>G Likely pathogenic ★★ same type
- FRMD7 p.Ala194Thr Pathogenic/Likely pathogenic ★★ same type
- FRMD7 p.Arg261Gln Pathogenic/Likely pathogenic ★★ same type
- FRMD7 p.Arg261Ter Pathogenic ★★ same type
- FRMD7 p.Arg304Ter Pathogenic ★★ same type
- FRMD7 p.Arg335Ter Pathogenic ★★ same type
- FRMD7 p.Gly24Arg Pathogenic ★★ 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/frmd7-p-ser558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown