Is HRAS p.Ile163= (c.489C>A) pathogenic?

HRAS p.Ile163= (c.489C>A) is classified Likely benign in HRAS (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-02). Absent from gnomAD v4.1; Associated with Costello syndrome.

What condition is associated with HRAS p.Ile163= (c.489C>A)?

HRAS p.Ile163= (c.489C>A) is associated with Costello syndrome (ClinVar).

How common is HRAS p.Ile163= (c.489C>A) in the general population?

HRAS p.Ile163= (c.489C>A) is absent from gnomAD v4.1 (gnomAD).

HRAS p.Ile163=

c.489C>A · rs2133982379 · VCV1122767

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Costello syndrome

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 -0.26	GERP -3.7, phastCons 0.017
Overall
CADD	0.845	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.Ile163=
Coding: c.489C>A
MANE Select: NM_005343
dbSNP: rs2133982379
Type: single nucleotide variant
Location: chr11:532717 (GRCh38)
Gene constraint: LOEUF 0.893 · pLI 0.02 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 92.50 · 256 PDB
Residue 163: an α-helix

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

Disease context

Costello syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

HRAS p.Ile163Met Uncertain significance ★ ⚠ same residue
HRAS p.Ile163Phe Uncertain significance ★ ⚠ same residue
HRAS p.Leu163fs Pathogenic/Likely pathogenic ★★ 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-ile163 (accessed [today's date]).

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