GAA p.Pro790=
c.2370T>A · rs2143924530 · VCV1790301
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -2.3 |
| Overall | ||
| CADD | 0.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GAA
- Protein
- p.Pro790=
- Coding
- c.2370T>A
- MANE Select
- NM_000152
- dbSNP
- rs2143924530
- Type
- single nucleotide variant
- Location
- chr17:80117638 (GRCh38)
- Gene constraint
- LOEUF 1.008 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.32 · 19 PDB
Similar variants
- GAA p.Pro790Ser Uncertain significance ★★ ⚠ same residue
- GAA c.2646+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GAA p.Arg190His Pathogenic/Likely pathogenic ★★ same condition
- GAA c.546+3G>A Uncertain significance ★★ same condition
- GAA p.Ala24Thr Uncertain significance ★★ ⚠ same condition
- GAA p.Ala625Thr Uncertain significance ★★ ⚠ same condition
- GAA p.Ala719Val Uncertain significance ★★ ⚠ same condition
- GAA p.Arg870Pro Uncertain significance ★★ ⚠ same condition
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/gaa-p-pro790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown