ARHGAP6 p.Ser693=
c.2079G>A · rs140286676 · VCV725186
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.188%, nfe)
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 -6.5 | GERP -5.3 |
| Overall | ||
| CADD | 0.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.188%
European (non-Finnish) · 1,681/894,894 alleles
Filtering AF
0.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.177%
Overall
0.152%
1,836/1,209,421 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.188% | 532 |
| Remaining individualsnot grpmax-eligible | 0.145% | 689 |
| South Asian | 0.0899% | 1,112 |
| Admixed American | 0.0284% | 3,516 |
| Finnishnot grpmax-eligible | 0.0257% | 3,886 |
| African / African-American | 0.0175% | 5,716 |
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
- ARHGAP6
- Protein
- p.Ser693=
- Coding
- c.2079G>A
- MANE Select
- NM_013427
- dbSNP
- rs140286676
- Type
- single nucleotide variant
- Location
- chrX:11144077 (GRCh38)
- Structure
- AlphaFold pLDDT 56.60
Similar variants
- ARHGAP6 c.589-9G>T Likely benign ★★ same type
- ARHGAP6 p.Ala533= Benign ★★ same type
- ARHGAP6 p.Leu413= Benign ★★ same type
- ARHGAP6 p.Leu526= Benign ★★ same type
- ARHGAP6 p.Leu841= Benign ★★ same type
- ARHGAP6 p.Tyr190= Benign ★★ same type
- HCCS c.521+7A>G Benign/Likely benign ★★ same type
- AMELX p.Ala16Asp 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/arhgap6-p-ser693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown