NM_005343.4:c.403C>G

HRAS · NP_005334.1:p.(Arg135Gly) · NM_005343.4

GRCh37: chr11:533500 G>C · GRCh38: chr11:533500 G>C

Gene: HRAS Transcript: NM_005343.4

Final call

VUS

PP2 supporting

Variant details

Gene

HRAS

Transcript

NM_005343.4

Protein

NP_005334.1:p.(Arg135Gly)

gnomAD AF

1.2394599425138478e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_005343.4:c.403C>G (p.Arg135Gly) is a missense variant in HRAS, a RASopathy gene. Only one criterion is met: PP2 at supporting strength, which applies to all RASopathy missense variants per the ClinGen RASopathy VCEP specification.

This variant is present in gnomAD v4.1 at extremely low frequency (2/1,613,606 alleles, AF ~0.00012%), with single alleles observed in South Asian and European (non-Finnish) populations. It is absent from gnomAD v2.1 and gnomAD-Canada.

This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (GeneDx, VCID 3371962) with criteria provided. No expert panel review or pathogenic classification exists.

Computational predictions are mixed: REVEL score 0.423 is intermediate, BayesDel score -0.136 leans benign, and SpliceAI predicts no splice impact (max delta 0.00). These do not converge on a consistent pathogenic or benign prediction.

Position 135 is not within a VCEP-approved PM1 functional domain (P-loop residues 10-17; Switch I residues 25-40) and is not identified as a statistically significant hotspot by cancerhotspots.org.

No functional studies have tested p.Arg135Gly in VCEP-approved assays (RAS Activation, MEK Activation, ERK Activation). The VCEP validation controls for HRAS are limited to G-domain residues (G12, G13, G60, K117, A146) and do not extend to position 135.

No de novo occurrences, segregation data, or case-control studies exist for this variant. No literature publications were identified that mention this specific variant.

With only PP2 (supporting) met and no other criteria fulfilled, this variant is classified as a Variant of Uncertain Significance (VUS) per the ACMG/AMP framework as modified by the ClinGen RASopathy VCEP.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	The ClinGen RASopathy VCEP explicitly designates PVS1 as Not Applicable because loss-of-function and/or haploinsufficiency has not been clearly identified as a disease mechanism for RASopathy genes. Additionally, NM_005343.4:c.403C>G (p.Arg135Gly) is a missense variant and does not fall into any null-variant category.	cspec
PS1	Not met	No evidence that p.Arg135Gly has been previously established as a pathogenic variant per VCEP criteria. This exact amino acid change has not been reported as pathogenic in germline RASopathy.	clinvar
PS2	Not met	No de novo occurrence data is available for this variant. The VCEP requires confirmed de novo (paternity confirmed) in a patient with RASopathy and no family history for PS2 at strong strength.
PS3	Not met	VCEP-approved functional assays (RAS Activation, MEK Activation, ERK Activation) exist for HRAS, but the specific variant p.Arg135Gly has not been tested in any approved study. The VCEP validation controls cover G-domain residues (G12, G13, G60, K117, A146) and do not extend to position 135 in the C-terminal region.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies
PS4	Not met	No confirmed independent occurrences of this variant in individuals with RASopathy phenotypes. A single ClinVar submission from GeneDx classifies it as Uncertain significance with condition 'Not Provided.' VCEP requires ≥1 (supporting), ≥3 (moderate), or ≥5 (strong) independent occurrences in affected individuals.	clinvar
PS5	N/A	PS5 is not a recognized ACMG/AMP criterion. It does not exist in the standard ACMG/AMP 2015 framework or in the ClinGen RASopathy VCEP specifications.
PM1	Not met	Position 135 is not within a VCEP-approved functional domain. The approved PM1 domains for HRAS are P-loop (residues 10-17) and Switch I (residues 25-40). Position 135 lies in the C-terminal portion of the G-domain, outside these domains. cancerhotspots.org does not identify this residue as a statistically significant hotspot.	vcep_alignment_with_pm1_domains_pptx
PM2	Not met	VCEP PM2 requires complete absence from all population databases. This variant is present in gnomAD v4.1 at 2/1,613,606 alleles (AF ~0.00012%), with 1 allele in South Asian and 1 in European (non-Finnish) populations. Presence in a population database disqualifies PM2 under the VCEP rule.	gnomad_v4
PM5	Not met	No candidate pathogenic missense variants at Arg135 were identified. PM5 requires a different pathogenic missense change at the same residue, established as pathogenic per VCEP criteria. No such comparator exists for Arg135 in the available data.	pm5_candidates
PM6	Not met	No de novo data (with or without parentage confirmation) is available for this variant. VCEP PM6 requires confirmed de novo without confirmation of paternity and maternity at moderate strength, or ≥2 independent occurrences at strong strength.
PP1	Not met	No co-segregation data is available. VCEP PP1 requires at least three informative meioses at supporting strength. No family studies or segregation data exist for this variant.
PP2	Met	PP2 is explicitly applicable to all RASopathy genes per the VCEP specification. HRAS is a RASopathy gene where missense variants are a common mechanism of disease, and this variant is a missense change (p.Arg135Gly).	cspec
PP3	Not met	Computational evidence is mixed and does not consistently support a deleterious effect. REVEL score 0.423 is intermediate (below the typical pathogenic threshold of 0.5), BayesDel score -0.136 leans benign, and SpliceAI max delta 0.00 predicts no splice impact. Multiple lines do not converge on a deleterious prediction.	revel bayesdel spliceai
PP4	N/A	The ClinGen RASopathy VCEP explicitly designates PP4 as Not Applicable. Patient phenotype specificity criteria are not used for RASopathies; PS4 proband counting is used instead.	cspec
PP5	N/A	The ClinGen RASopathy VCEP explicitly designates PP5 as not for use, per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BA1	Not met	VCEP BA1 threshold is allele frequency ≥0.05%. The highest observed population frequency is 0.0011% (South Asian, gnomAD v4.1), far below the BA1 threshold.	gnomad_v4
BS1	Not met	VCEP BS1 threshold is allele frequency ≥0.025%. The highest observed population frequency is 0.0011% (South Asian, gnomAD v4.1), far below the BS1 threshold.	gnomad_v4
BS2	Not met	VCEP BS2 specifically states that general population data should not be used; it requires well-phenotyped family members. No data on healthy adult individuals carrying this variant with confirmed RASopathy-negative clinical workup is available.
BS3	Not met	No functional studies demonstrating no damaging effect exist for p.Arg135Gly. VCEP-approved functional assays (RAS Activation, MEK Activation, ERK Activation) have not tested this variant.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies
BS4	Not met	No segregation data is available for this variant. VCEP BS4 requires at least one informative meiosis showing lack of segregation. No family studies exist.
BP1	N/A	VCEP BP1 applies specifically to truncating variants (nonsense, frameshift, canonical splice, initiation codon, multi-exon deletion) in genes without established LOF correlation to disease. This variant is a missense substitution, not a truncating variant, so BP1 is not applicable.	cspec
BP2	Not met	No data on trans or cis phase with a pathogenic variant is available. No co-occurrence data exists for this variant.
BP4	Not met	Computational evidence is mixed and does not consistently suggest no impact on the gene product. While SpliceAI (max delta 0.00) predicts no splice effect and BayesDel (-0.136) leans benign, REVEL (0.423) is intermediate and does not clearly support a benign interpretation. The multiple lines do not converge on a benign prediction sufficient to meet VCEP BP4 requirements.	revel bayesdel spliceai
BP5	Not met	No evidence that this variant has been observed in a case with an alternate molecular basis for disease. No co-occurring pathogenic variant in another RASopathy gene has been reported.
BP6	N/A	The ClinGen RASopathy VCEP explicitly designates BP6 as not for use, per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BP7	N/A	BP7 applies specifically to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. This variant (c.403C>G) is a missense substitution (p.Arg135Gly), not a synonymous variant.	cspec
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. This is a single-nucleotide substitution, not an in-frame indel.
PM3	N/A	VCEP explicitly designates PM3 as Not Applicable because this criterion applies to recessive disorders and is not applicable to the autosomal dominant RASopathies.	cspec
PM4	N/A	PM4 applies to in-frame deletions/insertions in non-repeat regions and stop-loss variants. This is a missense substitution, not a protein-length-altering variant.

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