RASA2 p.Gln491=
c.1473G>A · rs759211064 · VCV1671618
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0328%, eas)
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 -1.5 | GERP 0.89 |
| Overall | ||
| CADD | 0.761 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0328%
East Asian · 13/39,610 alleles
Filtering AF
0.0193%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0153%
Overall
0.000945%
14/1,481,642 alleles · ultra-rare
exomes 13/1,329,574 · genomes 1/152,068 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0328% | 3,047 |
| European (non-Finnish) | 9.03e-05% | 1,107,686 |
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
- RASA2
- Protein
- p.Gln491=
- Coding
- c.1473G>A
- MANE Select
- NM_006506
- dbSNP
- rs759211064
- Type
- single nucleotide variant
- Location
- chr3:141574057 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.63
- Residue 491
- the ras-gap domain
Similar variants
- RASA2 c.612-3C>T Uncertain significance ★★ same type
- RASA2 p.Ala360Gly Uncertain significance ★★ same type
- RASA2 p.Ala489Thr Uncertain significance ★★ same type
- RASA2 p.Ala503Ser Uncertain significance ★★ same type
- RASA2 p.Ala742Val Uncertain significance ★★ same type
- RASA2 p.Arg117His Uncertain significance ★★ same type
- RASA2 p.Arg310Gln Uncertain significance ★★ same type
- RASA2 p.Arg366Gln 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/rasa2-p-gln491 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown