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HRAS
Final classification
VUS
PM2
HRAS
c.7G>A
p.Glu3Lys
missense · exon 2

HRAS is a membrane-associated GTPase that acts as a molecular switch in cell signaling, cycling between active and inactive states as it binds and hydrolyzes GTP. It belongs to the RAS family of proto-oncogenes and helps transmit growth and survival signals through pathways such as MAPK and PI3K. Germline mutations in HRAS cause Costello syndrome, a developmental disorder marked by distinctive facial features, growth and cognitive problems, and a predisposition to tumors. Somatic HRAS mutations also drive many cancers, including cancers of the thyroid, bladder, and salivary glands.

This variant

Germline HRAS mutations cause Costello syndrome and somatic mutations drive cancers of the thyroid, bladder, and salivary glands, so a missense change in HRAS is potentially relevant to disease. This variant, p.(Glu3Lys), is absent from population databases but has no reported pathogenic, functional, or clinical evidence, so it cannot yet be assigned pathogenic or benign significance and remains a variant of uncertain significance pending further observations.

Transcript
NM_005343.4
HGVS · transcript:coding
NM_005343.4:c.7G>A
GRCh38
chr11:534316 C>T
GRCh37
chr11:534316 C>T
Basis Only PM2 (Supporting) is met under the ClinGen RASopathy HRAS v2.3 framework; no criteria-combination rule fires from a single Supporting criterion, so the result defaults to Uncertain Significance.
Only PM2 (Supporting) is met under the ClinGen RASopathy HRAS v2.3 framework; no criteria-combination rule fires from a single Supporting criterion, so the result defaults to Uncertain Significance.
Classification rationale
PM2 VUS
HRAS c.7G>A missense · exon 2

PM2 (Supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. With only this Supporting criterion met, no combination rule fires and the variant is classified as a variant of uncertain significance (VUS).

PM2 VUS
Gene diagram · NM_005343.4 · variants mapped to exon structure
HRAS NM_005343.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 16 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met (supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0.
The HRAS ClinGen RASopathy VCEP framework specifies PM2 at supporting strength when the variant is absent from controls in gnomAD.The variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
Assessed · not applied · 6 not met · 10 not assessed
Pathogenic
PS1 Not assessed: no pathogenic same-amino-acid comparator was found in HRAS; the paralog-gene comparison was not performed.
PS2 Not assessed: no proband-level de novo observation with parental testing or family history was available.
PS3 Not assessed: no functional assay data for p.(Glu3Lys) from a VCEP-approved assay type was identified.
PS4 Not assessed: no case-control enrichment data or affected-case counts were available for scoring.
PM1 Not met: codon 3 falls outside all four VCEP critical domains (P-loop, Switch I, Switch II, SAK).
PM5 Not met: no established pathogenic amino acid change at codon 3 was found in ClinVar.
PM6 Not assessed: no proband observation or parental genotypes establishing an assumed de novo event were available.
PP1 Not assessed: no affected or unaffected relatives or informative meioses were available for cosegregation scoring.
PP3 Not met: REVEL 0.412 is below the required 0.7 threshold.
Benign
BA1 Not met: absent from gnomAD, so allele frequency is below the 0.05% BA1 threshold.
BS1 Not met: absent from gnomAD, so allele frequency is below the 0.025% BS1 threshold.
BS2 Not assessed: no healthy-adult homozygote or heterozygote observations were available.
BS4 Not assessed: no family genotypes or informative meioses were available to evaluate non-segregation.
BP2 Not assessed: no in-trans observations, phase information, or qualifying allelic data were available.
BP4 Not met: REVEL 0.412 is above the <=0.3 BP4 threshold.
BP5 Not assessed: no alternate molecular diagnosis or second pathogenic variant in the patient was documented.
N/A · 11 PVS1 · PM3 · PM4 · PP2 · PP4 · PP5 · BS3 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.412. BayesDel score = -0.0436825.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. HRAS, a GTPase, is altered in a diverse range of cancers including head and neck squamous cell carcinoma, thyroid, and bladder cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54241514, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots