ARHGAP35 p.Ser1472=
c.4416G>A · VCV4943005
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.298%, amr)
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 -8.1 | GERP -3.7 |
| Overall | ||
| CADD | 0.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.298%
Admixed American · 178/59,832 alleles
Filtering AF
0.262%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.248%
Overall
0.0153%
246/1,611,786 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.298% | 336 |
| Remaining individualsnot grpmax-eligible | 0.0673% | 1,487 |
| African / African-American | 0.0134% | 7,446 |
| South Asian | 0.0022% | 45,426 |
| European (non-Finnish) | 0.00119% | 84,235 |
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
- ARHGAP35
- Protein
- p.Ser1472=
- Coding
- c.4416G>A
- MANE Select
- NM_004491
- Type
- single nucleotide variant
- Location
- chr19:47000604 (GRCh38)
- Gene constraint
- LOEUF 0.204 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.08 · 6 PDB
- Residue 1472
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- ARHGAP35 p.Arg1164= Benign ★★ same type
- ARHGAP35 p.Leu125= Benign ★★ same type
- ARHGAP35 p.Pro581= Benign ★★ same type
- ARHGAP35 p.Arg109Ter Likely pathogenic ★ same type
- ARHGAP35 p.Gln1067Ter Pathogenic ★ same type
- ARHGAP35 p.Gln1352Ter Pathogenic ★ same type
- ARHGAP35 p.Gln534Ter Likely pathogenic ★ same type
- ARHGAP35 p.Lys118Ter 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/arhgap35-p-ser1472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown