ARHGAP29 p.Arg53=
c.159G>A · VCV4901629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.97 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP -0.11, phastCons 0.93 |
| Overall | ||
| CADD | 11.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,054 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000248%
4/1,613,670 alleles · very rare
exomes 4/1,461,542 · genomes 0/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,527 |
| Admixed American | 0.00167% | 60,010 |
| European (non-Finnish) | 8.48e-05% | 1,179,702 |
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.Arg53=
- Coding
- c.159G>A
- MANE Select
- NM_004815
- Type
- single nucleotide variant
- Location
- chr1:94231453 (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-arg53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown