Is HRAS p.Ile139Phe (c.415A>T) pathogenic?

HRAS p.Ile139Phe (c.415A>T) is classified Uncertain significance in HRAS (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-05). AlphaMissense: likely pathogenic (0.7222); Absent from gnomAD v4.1; Associated with Costello syndrome.

What condition is associated with HRAS p.Ile139Phe (c.415A>T)?

HRAS p.Ile139Phe (c.415A>T) is associated with Costello syndrome (ClinVar).

How common is HRAS p.Ile139Phe (c.415A>T) in the general population?

HRAS p.Ile139Phe (c.415A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about HRAS p.Ile139Phe (c.415A>T)?

AlphaMissense predicts likely pathogenic (score 0.7222) — an in-silico prediction, not a clinical call.

HRAS p.Ile139Phe

c.415A>T · rs2133986598 · VCV1430912

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7222 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Costello syndrome

Computational evidence

Protein change
AlphaMissense	0.7222	likely pathogenic
REVEL	0.441	indeterminate
SaProt	LLR -14.18	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.94	GERP -1.1, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 1,164 bp · p 0.94 · regional, not allelic
Overall
CADD	20.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Ile139Phe
Coding: c.415A>T
MANE Select: NM_005343
dbSNP: rs2133986598
Type: single nucleotide variant
Location: chr11:533488 (GRCh38)
Gene constraint: LOEUF 0.893 · pLI 0.02 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 92.50 · 256 PDB

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.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
HRAS p.Gly138Ser Uncertain significance ★★★ ⚠ same condition
HRAS p.Ile93Val Uncertain significance ★★★ ⚠ same condition
HRAS p.Lys170Ter Uncertain significance ★★★ 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-ile139phe (accessed [today's date]).

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