FERMT3 p.Pro547=
c.1641C>T · VCV4912117
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -20 | GERP -4 |
| Overall | ||
| CADD | 0.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,884 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.00031%
5/1,610,946 alleles · very rare
exomes 5/1,458,586 · genomes 0/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,884 |
| European (non-Finnish) | 0.000339% | 295,003 |
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
- FERMT3
- Protein
- p.Pro547=
- Coding
- c.1641C>T
- MANE Select
- NM_031471
- Type
- single nucleotide variant
- Location
- chr11:64221111 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 83.80 · 6 PDB
- Residue 547
- the ferm domain; an α-helix
Similar variants
- FERMT3 p.Arg573Ter Pathogenic/Likely pathogenic ★★ same type
- FERMT3 p.Ala109Thr Uncertain significance ★★ ⚠ same type
- FERMT3 p.Ala338Val Uncertain significance ★★ ⚠ same type
- FERMT3 p.Ala570Thr Uncertain significance ★★ ⚠ same type
- FERMT3 p.Arg103Gln Uncertain significance ★★ ⚠ same type
- FERMT3 p.Arg111His Uncertain significance ★★ ⚠ same type
- FERMT3 p.Arg129His Uncertain significance ★★ ⚠ same type
- FERMT3 p.Arg179Leu 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/fermt3-p-pro547 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown