GPATCH4 p.His54Arg
c.161A>G · rs369352887 · VCV3101174
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0196%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.434 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain, 3 bp away · raw score · deltas |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 28.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0196%
European (non-Finnish) · 229/1,169,560 alleles
Filtering AF
0.0175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0166%
Overall
0.0151%
240/1,594,256 alleles · ultra-rare
exomes 232/1,442,046 · genomes 8/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0196% | 5,107 |
| Remaining individualsnot grpmax-eligible | 0.0162% | 6,168 |
| African / African-American | 0.00134% | 74,582 |
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.His54Arg
- Coding
- c.161A>G
- dbSNP
- rs369352887
- Type
- single nucleotide variant
- Location
- chr1:156598312 (GRCh38)
- Gene constraint
- LOEUF 1.669 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.52
- Residue 54
- the g-patch domain
Similar variants
- GPATCH4 p.Thr54Ile Uncertain significance ★ same residue
- 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
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-his54arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown