GEMIN4 p.Ser55=
c.165G>A · rs150160877 · VCV2647177
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.17%, nfe)
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 -3.8 |
| Overall | ||
| CADD | 0.033 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.17%
European (non-Finnish) · 2,001/1,179,880 alleles
Filtering AF
0.163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.132%
2,137/1,613,860 alleles · rare
exomes 2,006/1,461,666 · genomes 131/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.17% | 590 |
| Remaining individualsnot grpmax-eligible | 0.0816% | 1,225 |
| Finnishnot grpmax-eligible | 0.075% | 1,333 |
| Admixed American | 0.0283% | 3,530 |
| African / African-American | 0.0253% | 3,947 |
| Middle Eastern | 0.0165% | 6,062 |
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.Ser55=
- Coding
- c.165G>A
- MANE Select
- NM_015721
- dbSNP
- rs150160877
- Type
- single nucleotide variant
- Location
- chr17:747878 (GRCh38)
- Gene constraint
- LOEUF 0.947 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.54
Similar variants
- GEMIN4 p.Ser55Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown