ARFGAP3 p.Asp289=
c.867C>T · VCV4131170
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00483%, nfe)
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 -5.2 | GERP -3.1 |
| Overall | ||
| CADD | 1.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00483%
European (non-Finnish) · 57/1,179,542 alleles
Filtering AF
0.00378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00345%
Overall
0.00372%
60/1,612,730 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00483% | 20,694 |
| Admixed American | 0.00167% | 59,848 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,418 |
| African / African-American | 0.00134% | 74,790 |
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
- ARFGAP3
- Protein
- p.Asp289=
- Coding
- c.867C>T
- MANE Select
- NM_014570
- Type
- single nucleotide variant
- Location
- chr22:42817803 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.12 · 1 PDB
Similar variants
- ARFGAP3 p.Ala164Val Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala170Glu Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala234Thr Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala238Gly Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala262Thr Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala335Thr Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Ala426Ser Uncertain significance ★ ⚠ same type
- ARFGAP3 p.Arg15Cys 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/arfgap3-p-asp289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown