FRMD7 p.Val422=
c.1266C>G · rs1569339612 · VCV1631841
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, mid)
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 3.6 | GERP 2.9, phastCons 1 |
| Overall | ||
| CADD | 1.683 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
Middle Eastern · 1/4,349 alleles
Filtering AF
3.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000413%
5/1,210,391 alleles · ultra-rare
exomes 5/1,096,825 · genomes 0/113,566 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.023% | 4,349 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,798 |
| European (non-Finnish) | 0.000224% | 447,147 |
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.Val422=
- Coding
- c.1266C>G
- MANE Select
- NM_194277
- dbSNP
- rs1569339612
- Type
- single nucleotide variant
- Location
- chrX:132078751 (GRCh38)
- Structure
- AlphaFold pLDDT 62.31
Similar variants
- 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
- FRMD7 p.Gly296Arg 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-val422 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown