ARHGAP6 p.Ser928=
c.2784C>T · rs1469592263 · VCV2659984
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0247%, mid)
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 -0.79 | GERP -2.6 |
| Overall | ||
| CADD | 1.081 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0247%
Middle Eastern · 1/4,042 alleles
Filtering AF
0.00136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0011%
Overall
0.00166%
20/1,206,727 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0247% | 4,042 |
| European (non-Finnish) | 0.00212% | 47,059 |
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.Ser928=
- Coding
- c.2784C>T
- MANE Select
- NM_013427
- dbSNP
- rs1469592263
- Type
- single nucleotide variant
- Location
- chrX:11139004 (GRCh38)
- Structure
- AlphaFold pLDDT 56.60
- Residue 928
- a modified residue (phosphoserine); the 'disordered' region
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-ser928 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown