VAV1 p.Phe86=
c.258C>T · rs534653385 · VCV2892967
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, mid)
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 -4 | GERP -3.6 |
| Overall | ||
| CADD | 5.403 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,084 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00781%
126/1,614,042 alleles · ultra-rare
exomes 118/1,461,860 · genomes 8/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,217 |
| South Asian | 0.0274% | 3,643 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| Admixed American | 0.00667% | 14,999 |
| European (non-Finnish) | 0.00653% | 15,325 |
| African / African-American | 0.00534% | 18,731 |
| East Asian | 0.00445% | 22,447 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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
- VAV1
- Protein
- p.Phe86=
- Coding
- c.258C>T
- MANE Select
- NM_005428
- dbSNP
- rs534653385
- Type
- single nucleotide variant
- Location
- chr19:6820755 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63 · 10 PDB
- Residue 86
- the calponin-homology (ch) domain
Similar variants
- VAV1 p.Ala168Val Uncertain significance ★★ ⚠ same type
- VAV1 p.Ala362Thr Uncertain significance ★★ ⚠ same type
- VAV1 p.Ala734Thr Uncertain significance ★★ same type
- VAV1 p.Arg15Gln Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg179Ser Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg195His Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg282His Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg296His 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/vav1-p-phe86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown