ARHGAP9 p.Ala69=
c.207T>G · rs58668629 · VCV773024
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.91%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.045 | GERP -1.9, phastCons 0.76 |
| Overall | ||
| CADD | 8.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.91%
African / African-American · 5,179/74,968 alleles
Filtering AF
6.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.69%
Overall
0.386%
6,228/1,614,084 alleles · common
exomes 3,360/1,461,894 · genomes 2,868/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.91% | 14 |
| Middle Eastern | 0.594% | 168 |
| Admixed American | 0.58% | 172 |
| Remaining individualsnot grpmax-eligible | 0.549% | 182 |
| European (non-Finnish) | 0.0259% | 3,856 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0236% | 4,230 |
| South Asian | 0.00988% | 10,120 |
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
- ARHGAP9
- Protein
- p.Ala69=
- Coding
- c.207T>G
- MANE Select
- NM_032496
- dbSNP
- rs58668629
- Type
- single nucleotide variant
- Location
- chr12:57479200 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.99 · 3 PDB
- Residue 69
- the sh3 domain
Similar variants
- MARS1 c.-18C>T Uncertain significance ★★ same type
- MARS1 p.Glu27Lys Uncertain significance ★★ ⚠ same type
- MARS1 p.Gly11Ser Uncertain significance ★★ ⚠ same type
- MARS1 p.Gly24Ala Uncertain significance ★★ ⚠ same type
- MARS1 p.Gly24Ser Uncertain significance ★★ ⚠ same type
- MARS1 p.Thr32Ser Uncertain significance ★★ ⚠ same type
- MARS1 p.Val5Met Uncertain significance ★★ ⚠ same type
- MARS1 c.109+112A>G Benign ★★ 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/arhgap9-p-ala69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown