GEMIN5 p.Arg671=
c.2013G>T · VCV3771548
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.33%, 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 -2.3 | GERP -4.1 |
| Overall | ||
| CADD | 3.345 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.33%
East Asian · 148/44,890 alleles
Filtering AF
0.286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.27%
Overall
0.0101%
163/1,613,916 alleles · rare
exomes 139/1,461,764 · genomes 24/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.33% | 303 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
| European (non-Finnish) | 8.47e-05% | 1,179,994 |
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
- GEMIN5
- Protein
- p.Arg671=
- Coding
- c.2013G>T
- MANE Select
- NM_015465
- Type
- single nucleotide variant
- Location
- chr5:154911881 (GRCh38)
- Gene constraint
- LOEUF 0.839 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.17 · 16 PDB
- Residue 671
- an α-helix; a UniProt-annotated variant site (in nedcam)
Similar variants
- GEMIN5 p.Arg671Gln Likely benign ★ same residue
- GEMIN5 p.Arg260Ter Likely pathogenic ★★ same type
- GEMIN5 p.Ile988Phe Likely pathogenic ★★ same type
- GEMIN5 p.Leu1367Pro Likely pathogenic ★★ same type
- GEMIN5 p.Arg1284His Uncertain significance ★★ ⚠ same type
- GEMIN5 p.Glu209Lys Uncertain significance ★★ ⚠ same type
- GEMIN5 p.Leu1127Pro Uncertain significance ★★ ⚠ same type
- GEMIN5 p.Leu1359His 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/gemin5-p-arg671 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown