ARHGAP29 p.Phe117=
c.351C>T · rs764782951 · VCV756054
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0352%, mid)
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 3.9 | GERP 0.64, phastCons 1 |
| Overall | ||
| CADD | 12.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0352%
Middle Eastern · 2/5,686 alleles
Filtering AF
0.00617%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000249%
4/1,605,012 alleles · ultra-rare
exomes 4/1,452,804 · genomes 0/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0352% | 2,843 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,192 |
| European (non-Finnish) | 8.5e-05% | 1,176,988 |
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
- ARHGAP29
- Protein
- p.Phe117=
- Coding
- c.351C>T
- MANE Select
- NM_004815
- dbSNP
- rs764782951
- Type
- single nucleotide variant
- Location
- chr1:94209340 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.41
Similar variants
- ARHGAP29 p.Gln19His Uncertain significance ★★ ⚠ same type
- ARHGAP29 p.Met318Val Uncertain significance ★★ ⚠ same type
- ARHGAP29 p.Trp533Arg Uncertain significance ★★ ⚠ same type
- ARHGAP29 c.2905+8G>A Benign/Likely benign ★★ same type
- ARHGAP29 p.Ala959= Benign ★★ same type
- ARHGAP29 p.Arg798Gln Likely benign ★★ same type
- ARHGAP29 p.Gly1115= Benign/Likely benign ★★ same type
- ARHGAP29 p.Leu163= Likely 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/arhgap29-p-phe117 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown