GPATCH4 p.Arg288Gly
c.862A>G · rs140797137 · VCV2215556
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.091 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -2.9, phastCons 0.013 |
| Overall | ||
| CADD | 20.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
Admixed American · 28/60,014 alleles
Filtering AF
0.0331%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0286%
Overall
0.0237%
383/1,614,182 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0467% | 2,143 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| European (non-Finnish) | 0.027% | 3,699 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.00625% | 16,011 |
| African / African-American | 0.00533% | 18,765 |
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.Arg288Gly
- Coding
- c.862A>G
- dbSNP
- rs140797137
- Type
- single nucleotide variant
- Location
- chr1:156595464 (GRCh38)
- Gene constraint
- LOEUF 1.669 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.52
- Residue 288
- 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-arg288gly (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown