Is HRAS p.Gln99= (c.297G>A) pathogenic?

HRAS p.Gln99= (c.297G>A) is classified Likely benign in HRAS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-08-17). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with HRAS p.Gln99= (c.297G>A)?

HRAS p.Gln99= (c.297G>A) is associated with Cardiovascular phenotype, Costello syndrome (ClinVar).

How common is HRAS p.Gln99= (c.297G>A) in the general population?

HRAS p.Gln99= (c.297G>A) is absent from gnomAD v4.1 (gnomAD).

HRAS p.Gln99=

c.297G>A · rs199656012 · VCV1138050

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.28	acceptor loss, 1 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 2.1	GERP 0.67, phastCons 1
Overall
CADD	8.046	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: HRAS
Protein: p.Gln99=
Coding: c.297G>A
MANE Select: NM_005343
dbSNP: rs199656012
Type: single nucleotide variant
Location: chr11:533606 (GRCh38)
Gene constraint: LOEUF 0.893 · pLI 0.02 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 92.50 · 256 PDB
Residue 99: an α-helix

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Costello syndrome

Similar variants

HRAS p.Gln99Glu Uncertain significance ★ ⚠ same residue
HRAS p.Gln99His Uncertain significance ★ ⚠ same residue
HRAS p.Gln99Ter Uncertain significance ★ same residue
HRAS p.Ala59Thr Likely pathogenic ★★★ same condition
HRAS p.Gly12Ser Pathogenic ★★★ same condition
HRAS p.Gly13Cys Pathogenic ★★★ same condition
HRAS p.Lys117Arg Pathogenic ★★★ same condition
HRAS p.Thr58Ile Pathogenic ★★★ same condition

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/hras-p-gln99 (accessed [today's date]).

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