ARHGAP44 p.Pro548=
c.1644G>A · rs749532745 · VCV736658
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00436%, nfe)
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 -2.3 | GERP -3.8 |
| Overall | ||
| CADD | 5.119 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00436%
European (non-Finnish) · 50/1,146,862 alleles
Filtering AF
0.00335%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00303%
Overall
0.00329%
51/1,548,646 alleles · very rare
exomes 46/1,396,590 · genomes 5/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00436% | 22,937 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,918 |
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
- ARHGAP44
- Protein
- p.Pro548=
- Coding
- c.1644G>A
- MANE Select
- NM_014859
- dbSNP
- rs749532745
- Type
- single nucleotide variant
- Location
- chr17:12974191 (GRCh38)
- Gene constraint
- LOEUF 0.605 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.39
- Residue 548
- the 'disordered' region
Similar variants
- ARHGAP44 p.Pro548Leu Uncertain significance ★ ⚠ same residue
- ARHGAP44 p.Gln414= Benign ★★ same type
- ARHGAP44 c.198+1G>A Uncertain significance ★ same type
- ARHGAP44 p.Ala128Val Uncertain significance ★ ⚠ same type
- ARHGAP44 p.Ala172Val Uncertain significance ★ ⚠ same type
- ARHGAP44 p.Ala186Thr Uncertain significance ★ ⚠ same type
- ARHGAP44 p.Ala304Val Uncertain significance ★ ⚠ same type
- ARHGAP44 p.Ala366Thr Uncertain significance ★ ⚠ 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/arhgap44-p-pro548 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown