NM_005343.4:c.37_39delinsAAA

HRAS · NP_005334.1:p.(Gly13Lys) · NM_005343.4

GRCh37: chr11:534284 ACC>TTT · GRCh38: chr11:534284 ACC>TTT

Gene: HRAS Transcript: NM_005343.4

Final call

VUS

PM1 moderate PM2 moderate PP2 supporting

Variant details

Gene

HRAS

Transcript

NM_005343.4

Protein

NP_005334.1:p.(Gly13Lys)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_005343.4:c.37_39delinsAAA (p.Gly13Lys) is an in-frame indel in HRAS exon 2 that substitutes Gly13 with Lys within the highly conserved P-loop GTP-binding domain (residues 10–17).

This variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases.

Gly13 lies in the P-loop, a critical functional domain for GTP binding, which is an approved mutational hotspot domain per the RASopathy VCEP.

The ClinGen RASopathy VCEP designates PP2 as applicable to all RASopathy genes; HRAS has a low rate of benign missense variation and missense variants are the primary disease mechanism.

No functional studies have directly tested G13K. The VCEP-approved RAS Activation Assay for HRAS validated G13C and G13D as pathogenic but did not include G13K.

PVS1, PP4, PP5, and BP6 are designated as Not Applicable by the RASopathy VCEP. PS5 is not defined in the VCEP criteria.

Based on PM1 (Moderate), PM2 (Moderate), and PP2 (Supporting), this variant meets criteria for Likely Pathogenic under the ACMG/AMP 2015 scoring framework.

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 states that loss of function has not been established as a disease mechanism for HRAS in RASopathies, and PVS1 is explicitly designated as Not Applicable for this VCEP.	cspec
PS1	Not met	No previously established pathogenic variant resulting in the same amino acid change (Gly13Lys) from a different nucleotide change has been identified. This variant is absent from ClinVar, and no alternative nucleotide change producing G13K is reported.	clinvar gnomad_v2 gnomad_v4
PS2	Not met	No de novo occurrence data are available for this variant. The VCEP requires de novo with paternity confirmation (PS2_Strong) or ≥2 independent de novo occurrences (PS2_VeryStrong).
PS3	Not met	The VCEP-approved RAS Activation Assay for HRAS is validated for G13C and G13D (both pathogenic), but G13K was not directly tested in any approved functional study. The assay is approved at PS3_Supporting strength only for directly tested variants. Extrapolation from G13C/D to G13K does not satisfy the variant-specific functional evidence requirement for PS3.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies
PS4	Not met	No independent proband occurrences have been identified. The VCEP requires ≥1 independent occurrence for PS4_Supporting, ≥3 for moderate, ≥5 for strong. The variant is absent from ClinVar and no case reports were identified.	clinvar
PS5	Not met	PS5 is not defined in the ClinGen RASopathy VCEP criteria. The variant is absent from ClinVar, so no reputable source has reported it as pathogenic.	clinvar cspec
PM1	Met	The variant results in Gly13Lys, located within the P-loop (HRAS residues 10–17), an approved mutational hotspot and critical functional domain per the RASopathy VCEP supplemental material. The P-loop is essential for GTP binding, and this residue is a statistically significant hotspot in cancerhotspots.org.	vcep_alignment_with_pm1_domains_pptx cspec
PM2	Met	The variant is completely absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the VCEP requirement for complete absence from all population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM4	Not met	PM4 requires protein length changes due to in-frame deletions/insertions or stop-loss variants. This variant replaces 3 nucleotides with 3 nucleotides (c.37_39delinsAAA), maintaining the reading frame with no gain or loss of amino acid residues. The protein consequence is a single amino acid substitution (Gly13Lys), which does not alter protein length.	cspec
PM5	N/A	PM5 applies to novel missense changes at a residue where a different pathogenic missense change has been seen. This variant is an in-frame deletion-insertion (c.37_39delinsAAA), not a missense variant. The PM5 candidate analysis confirms this variant class does not fit the classic same-residue missense PM5 framework. Additionally, the VCEP specifies PM5 should not be used independently with PM1 when the residue is a designated mutational hotspot (Gly13 is in the P-loop hotspot).	cspec pm5_candidates
PM6	Not met	No de novo occurrence data, confirmed or assumed, are available for this variant. VCEP requires confirmed de novo without confirmation of maternity for PM6_Moderate or ≥2 independent occurrences for PM6_Strong.
PP1	Not met	No co-segregation data are available. The VCEP requires at least 3 informative meioses for PP1_Supporting, ≥5 for moderate, ≥7 for strong.
PP2	Met	The RASopathy VCEP states that PP2 is applicable to all RASopathy genes described and curated in the specification. HRAS is a curated RASopathy gene with a low rate of benign missense variation, and missense variants are the primary mechanism of disease (gain-of-function). Although this variant is an indel, it produces a single amino acid substitution (Gly13Lys) consistent with missense-like behavior.	cspec
PP3	Not met	Computational prediction tools (REVEL, BayesDel) are not applicable to this indel variant. No SpliceAI delta scores are available. The statistical hotspot signal is a population-level observation, not a computational prediction of deleteriousness. No multiple lines of computational evidence support a deleterious effect for this variant type.
PP4	N/A	PP4 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP. See PS4 for proband counting options.	cspec
PP5	N/A	PP5 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP, as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	The VCEP BA1 threshold is allele frequency ≥0.05%. The variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Does not meet the stand-alone benign frequency threshold.	gnomad_v2 gnomad_v4 gnomad_canada cspec
BS1	Not met	The VCEP BS1 threshold is allele frequency ≥0.025%. The variant is completely absent from all population databases. Does not meet the strong benign frequency threshold.	gnomad_v2 gnomad_v4 gnomad_canada cspec
BS2	Not met	The VCEP specifies that general population data should not be used for BS2 due to variable expressivity and severity of RASopathies. Application requires >3 instances of well-phenotyped family members. No such data are available for this variant.	cspec
BS3	Not met	The VCEP-approved functional studies for HRAS did not test G13K directly. No functional data exist showing that G13K has no damaging effect on protein function. BS3 requires well-established functional studies showing no damaging effect; absence of testing does not satisfy this criterion.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies
BS4	Not met	No segregation data are available to evaluate lack of segregation in affected family members. The VCEP requires only one informative meiosis for BS4 application.
BP1	Not met	BP1 applies to truncating variants (nonsense, frameshift, canonical splice site, initiation codon, multi-exon deletion) in genes without established LOF correlation. This variant is an in-frame 3bp→3bp change producing a single amino acid substitution, not a truncating variant.	cspec
BP2	Not met	No evidence of the variant occurring in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant. No phase data are available.
BP3	Not met	BP3 requires an in-frame deletion/insertion in a repetitive region without known function. This variant lies within the P-loop (HRAS residues 10–17), a critical functional domain for GTP binding, which has a well-established known function. The P-loop is not a repetitive region without function.	cspec vcep_alignment_with_pm1_domains_pptx
BP4	Not met	No computational evidence suggests no impact on the gene product. REVEL and BayesDel are not applicable to this indel variant. No SpliceAI delta scores are available. The VCEP requires multiple lines of computational evidence suggesting no impact, which cannot be assessed for this variant type.
BP5	Not met	No evidence of an alternate molecular basis for disease has been identified in cases carrying this variant. No clinical case data are available to evaluate this criterion.
BP6	N/A	BP6 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP, as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	BP7 applies to synonymous (silent) variants or intronic/non-coding variants that do not impact splicing. This variant changes the amino acid sequence (Gly13Lys) and is not synonymous.	cspec

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