FRMD7 p.Phe497=
c.1491T>C · rs1927695620 · VCV1920869
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00173%, 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 4.1 | GERP 4.4, phastCons 1 |
| Overall | ||
| CADD | 7.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00173%
African / African-American · 1/57,744 alleles
Overall
8.25e-05%
1/1,211,513 alleles · very rare
exomes 1/1,097,973 · genomes 0/113,540 · joint denominator
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.Phe497=
- Coding
- c.1491T>C
- MANE Select
- NM_194277
- dbSNP
- rs1927695620
- Type
- single nucleotide variant
- Location
- chrX:132078526 (GRCh38)
- Structure
- AlphaFold pLDDT 62.31
Similar variants
- FRMD7 p.Phe497Ser 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-phe497 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown