GPATCH4 p.Gly309Arg
c.925G>A · VCV3521503
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP 0.82 |
| Overall | ||
| CADD | 14.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,970 alleles
Overall
0.000186%
3/1,613,876 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,970 |
| African / African-American | 0.00134% | 74,870 |
| European (non-Finnish) | 8.47e-05% | 1,179,998 |
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
- GPATCH4
- Protein
- p.Gly309Arg
- Coding
- c.925G>A
- Type
- single nucleotide variant
- Location
- chr1:156595416 (GRCh38)
- Gene constraint
- LOEUF 1.669 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.52
- Residue 309
- the 'disordered' region
Similar variants
- GPATCH4 c.348+115G>A Uncertain significance ★ same type
- GPATCH4 c.-65A>C Uncertain significance ★ same type
- GPATCH4 c.-74G>C Uncertain significance ★ same type
- GPATCH4 c.-79G>C Uncertain significance ★ same type
- GPATCH4 p.Ala162Thr Uncertain significance ★ same type
- GPATCH4 p.Ala174Pro Uncertain significance ★ same type
- GPATCH4 p.Ala219Val Uncertain significance ★ same type
- GPATCH4 p.Ala316Val 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/gpatch4-p-gly309arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown