GPAA1 p.Arg541=
c.1623G>A · rs182775098 · VCV1666405
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, afr)
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 8.3 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 15.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
African / African-American · 968/74,926 alleles
Filtering AF
1.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2%
Overall
0.0663%
1,064/1,605,574 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.29% | 77 |
| Admixed American | 0.0819% | 1,221 |
| Remaining individualsnot grpmax-eligible | 0.0579% | 1,727 |
| Middle Eastern | 0.0496% | 2,015 |
| South Asian | 0.0033% | 30,294 |
| European (non-Finnish) | 0.000425% | 235,065 |
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
- GPAA1
- Protein
- p.Arg541=
- Coding
- c.1623G>A
- MANE Select
- NM_003801
- dbSNP
- rs182775098
- Type
- single nucleotide variant
- Location
- chr8:144085882 (GRCh38)
- Gene constraint
- LOEUF 1.077 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.48 · 4 PDB
- Residue 541
- an α-helix
Similar variants
- GPAA1 p.Arg541Gln Uncertain significance ★★ ⚠ same residue
- GPAA1 p.Arg541Trp Uncertain significance ★ ⚠ same residue
- GPAA1 c.1165-1C>T Likely pathogenic ★★ same type
- GPAA1 c.366+1G>A Likely pathogenic ★★ same type
- GPAA1 c.616+1G>T Likely pathogenic ★★ same type
- GPAA1 p.Arg215Ter Pathogenic/Likely pathogenic ★★ same type
- GPAA1 p.Leu291Pro Likely pathogenic ★★ same type
- GPAA1 p.Ser419Ter Pathogenic/Likely pathogenic ★★ 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/gpaa1-p-arg541 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown