Is VAV1 p.Phe97= (c.291T>C) pathogenic?

VAV1 p.Phe97= (c.291T>C) is classified Likely benign in VAV1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-16). Absent from gnomAD v4.1.

How common is VAV1 p.Phe97= (c.291T>C) in the general population?

VAV1 p.Phe97= (c.291T>C) is absent from gnomAD v4.1 (gnomAD).

VAV1 p.Phe97=

c.291T>C · rs2144767762 · VCV1658971

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -5.7	GERP -3.5
Overall
CADD	5.917	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: VAV1
Protein: p.Phe97=
Coding: c.291T>C
MANE Select: NM_005428
dbSNP: rs2144767762
Type: single nucleotide variant
Location: chr19:6820788 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.63 · 10 PDB
Residue 97: the calponin-homology (ch) domain; an α-helix

Full VAV1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-phe97 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown