FERMT1 p.Pro102=
c.306G>A · rs141850118 · VCV1105699
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0575%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -4 |
| Overall | ||
| CADD | 0.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0575%
European (non-Finnish) · 679/1,180,038 alleles
Filtering AF
0.0539%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0525%
Overall
0.046%
743/1,614,132 alleles · ultra-rare
exomes 686/1,461,880 · genomes 57/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0575% | 1,738 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Finnishnot grpmax-eligible | 0.0297% | 3,370 |
| Admixed American | 0.0133% | 7,502 |
| African / African-American | 0.00933% | 10,717 |
| East Asian | 0.00223% | 44,880 |
| South Asian | 0.0022% | 45,537 |
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
- FERMT1
- Protein
- p.Pro102=
- Coding
- c.306G>A
- MANE Select
- NM_017671
- dbSNP
- rs141850118
- Type
- single nucleotide variant
- Location
- chr20:6115890 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.14
- Residue 102
- the ferm domain
Similar variants
- FERMT1 p.Pro102Leu Uncertain significance ★★ ⚠ same residue
- FERMT1 c.1371+4A>G Pathogenic ★★ same type
- FERMT1 c.532+1G>A Likely pathogenic ★★ same type
- FERMT1 p.Arg110Ter Pathogenic ★★ same type
- FERMT1 p.Arg271Ter Pathogenic ★★ same type
- FERMT1 p.Arg288Ter Pathogenic ★★ same type
- FERMT1 p.Glu304Ter Pathogenic ★★ same type
- FERMT1 p.Trp298Ter 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/fermt1-p-pro102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown