GEMIN4 p.Phe196=
c.588C>T · VCV4932382
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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 3.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,882 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00105%
17/1,613,734 alleles · very rare
exomes 16/1,461,556 · genomes 1/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,882 |
| Finnishnot grpmax-eligible | 0.00156% | 63,954 |
| European (non-Finnish) | 0.00127% | 78,655 |
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
- GEMIN4
- Protein
- p.Phe196=
- Coding
- c.588C>T
- MANE Select
- NM_015721
- Type
- single nucleotide variant
- Location
- chr17:747455 (GRCh38)
- Gene constraint
- LOEUF 0.947 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.54
Similar variants
- GEMIN4 p.Trp818Arg Pathogenic/Likely pathogenic ★★ same type
- GEMIN4 p.Ala186Val Uncertain significance ★★ ⚠ same type
- GEMIN4 p.Arg91Gln Uncertain significance ★★ ⚠ same type
- GEMIN4 p.Gln1032Ter Uncertain significance ★★ same type
- GEMIN4 p.Gly814Glu Uncertain significance ★★ ⚠ same type
- GEMIN4 p.Ile406Val Uncertain significance ★★ ⚠ same type
- GEMIN4 p.Leu178Val Uncertain significance ★★ ⚠ same type
- GEMIN4 p.Ser755Phe 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/gemin4-p-phe196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown