RASGRP2 p.Pro358=
c.1074C>T · VCV3727703
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00546%, 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 -9.6 | GERP -3.9 |
| Overall | ||
| CADD | 1.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00546%
European (non-Finnish) · 64/1,172,368 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00398%
Overall
0.00463%
74/1,596,628 alleles · very rare
exomes 65/1,444,410 · genomes 9/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00546% | 18,318 |
| Remaining individualsnot grpmax-eligible | 0.00486% | 20,569 |
| South Asian | 0.00451% | 22,170 |
| African / African-American | 0.00402% | 24,856 |
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.Pro358=
- Coding
- c.1074C>T
- MANE Select
- NM_001098671
- Type
- single nucleotide variant
- Location
- chr11:64736774 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.48 · 2 PDB
- Residue 358
- 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-pro358 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown