RASGRP2 p.Phe338=
c.1014T>C · VCV4707504
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 0.98 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 9.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,922 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00031%
5/1,612,928 alleles · very rare
exomes 2/1,460,736 · genomes 3/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,730 |
| European (non-Finnish) | 8.47e-05% | 1,179,952 |
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
- RASGRP2
- Protein
- p.Phe338=
- Coding
- c.1014T>C
- MANE Select
- NM_001098671
- Type
- single nucleotide variant
- Location
- chr11:64736834 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.48 · 2 PDB
- Residue 338
- the ras-gef domain; a UniProt-annotated variant site (in bdplt18); a UniProt-annotated variant site (in bdplt18; lack of mutant protein in platelets from a patient homozygous for the mutation); an α-helix
Similar variants
- RASGRP2 p.Gly305Asp Likely pathogenic ★★ same type
- RASGRP2 p.Arg387Gly Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Arg593His Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Asn330Lys Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Gly331Arg Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Gly492Trp Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Leu107Ile Uncertain significance ★★ ⚠ same type
- RASGRP2 p.Lys55Met 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/rasgrp2-p-phe338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown