KRAS c.34G>C, p.Gly12Arg

Reasoning

KRAS p.Gly12Arg is at residue 12. The KRAS VCEP restricts PM1 to approved critical functional domains and lists the P-loop as amino acids 10-17; residue 12 therefore lies within an approved PM1 domain. The governing alignment file confirms the P-loop region is HRAS/KRAS/NRAS 10-17 and shows the corresponding paralog alignment. The file was searched for c.34G>C, p.Gly12Arg, and p.G12R with no literal variant entry, but the domain-range evidence directly establishes eligibility.

VCEP rule

Applicable only to critical and well-established functional domains available in the supplementary table (P-loop [AA 10-17], SW1 [AA 25-40], SW2 [AA 57-64], SAK [AA 145-156]). Not applicable to specific amino acid residues (see PM5).

Evidence considered

• The KRAS VCEP PM1 rule limits PM1 to the P-loop (AA 10-17), SW1 (AA 25-40), SW2 (AA 57-64), and SAK (AA 145-156), and excludes specific amino-acid residues as a PM1 route.
• The variant is NP_004976.2:p.(Gly12Arg), placing the altered residue at amino acid 12 within the approved P-loop range 10-17.
• Alignment-with-PM1-domains.pptx.pdf states that HRAS, KRAS, and NRAS share residue numbering across the shaded regions and identifies the P-loop as 10-17.
• Alignment-with-PM1-domains.pptx.pdf was searched for c.34G>C, p.Gly12Arg, and p.G12R; no literal entry was found.

Still missing

• No literal c.34G>C, p.Gly12Arg, or p.G12R entry was found when Alignment-with-PM1-domains.pptx.pdf was searched.

Sources

Reasoning

The governing VCEP applies PM2 at supporting strength when the variant is absent from controls in gnomAD. NM_004985.5:c.34G>C is absent from gnomAD v2.1 non-cancer exomes and gnomAD v4.1, while the gnomAD v2.1 all-comers exome record has AC=0/249272 and AF=0.0% with zero homozygotes; PM2 Supporting is met.

VCEP rule

The variant must be absent from controls (gnomAD).

Evidence considered

• ClinGen RASopathy Expert Panel KRAS specification v2.3, PM2 rule: The variant must be absent from controls (gnomAD).
• gnomAD v2.1 non-cancer exome-only source: variant absent.
• gnomAD v4.1: variant absent.
• gnomAD v2.1 all-comers exome record for 12-25398285-C-G: AC=0, AN=249272, AF=0.0%, homozygotes=0; African/African American subgroup AC=0, AN=16042, AF=0.0%, homozygotes=0.

Sources

Reasoning

The variant is missense, NM_004985.5:c.34G>C (p.Gly12Arg). The governing KRAS VCEP rule applies the missense PP3 path using REVEL >= 0.7. The REVEL score is 0.821, meeting the VCEP threshold, so PP3 is met at Supporting strength. The VCEP's separate splicing-impact clause is not needed for this missense-path determination, and the SpliceAI result is not used as an additional PP3/BP4 criterion.

VCEP rule

For missense variants: REVEL >= 0.7. For splicing impact, predicted outcome must match disease mechanism.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS v2.3 PP3 rule: missense variants use REVEL >= 0.7; the variant is NM_004985.5:c.34G>C (p.Gly12Arg), a missense variant.
• Local REVEL predictor lookup: REVEL score 0.821 for NM_004985.5:c.34G>C, above the VCEP threshold of 0.7.

Sources

Reasoning

The KRAS NM_004985.5:c.34G>C (p.Gly12Arg) variant has a gnomAD v2.1 filtering allele frequency of 0/249272 alleles (0.00000%) and is absent from gnomAD v4.1. The observed frequency is below the governing VCEP stand-alone BA1 threshold of 0.05%; therefore BA1 is not met. The gnomAD v2.1 non-cancer exome-only query also reports the variant as absent, but no frequency threshold is reached in any applicable population source.

VCEP rule

GnomAD filtering allele frequency ≥0.05%.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS specification v2.3, BA1 rule: GnomAD filtering allele frequency ≥0.05%.
• gnomAD v2.1, variant 12-25398285-C-G: exome AC=0, AN=249272, AF=0.0%, homozygotes=0; African/African American subgroup AC=0, AN=16042, AF=0.0%, homozygotes=0.
• gnomAD v4.1, variant chr12-25245351-C-G: absent.
• gnomAD v2.1 non-cancer exome-only source: variant absent.

Sources

Reasoning

The KRAS NM_004985.5:c.34G>C (p.Gly12Arg) variant has a gnomAD v2.1 filtering allele frequency of 0/249272 alleles (0.00000%) and is absent from gnomAD v4.1. This is below the governing VCEP BS1 threshold of 0.025%; therefore BS1 is not met. The gnomAD v2.1 non-cancer exome-only query also reports the variant as absent.

VCEP rule

GnomAD filtering allele frequency ≥0.025%.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS specification v2.3, BS1 rule: GnomAD filtering allele frequency ≥0.025%.
• gnomAD v2.1, variant 12-25398285-C-G: exome AC=0, AN=249272, AF=0.0%, homozygotes=0; African/African American subgroup AC=0, AN=16042, AF=0.0%, homozygotes=0.
• gnomAD v4.1, variant chr12-25245351-C-G: absent.
• gnomAD v2.1 non-cancer exome-only source: variant absent.

Sources

Reasoning

The variant is missense, so the governing KRAS VCEP BP4 missense path uses REVEL <= 0.3. The REVEL score is 0.821, which exceeds the VCEP benign threshold; therefore BP4 is not met. SpliceAI is not used to replace or supplement the VCEP's named missense predictor path.

VCEP rule

For missense variants: REVEL <=0.3.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS v2.3 BP4 rule: missense variants use REVEL <= 0.3; the variant is NM_004985.5:c.34G>C (p.Gly12Arg), a missense variant.
• Local REVEL predictor lookup: REVEL score 0.821 for NM_004985.5:c.34G>C, above the VCEP threshold of 0.3, so it does not support BP4.

Sources

Reasoning

The KRAS VCEP requires the same amino-acid change to have been previously established as pathogenic, regardless of nucleotide change. The available evidence identifies KRAS p.G12R in functional and cancer-resistance studies, but does not establish a pathogenic alternate nucleotide change encoding p.G12R. The required governing VCEP file, Alignment-with-PM1-domains.pptx.pdf, was searched for c.34G>C, p.Gly12Arg, and p.G12R with no literal variant entry; no qualifying pathogenic comparator was identified in the available case evidence.

VCEP rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in _HRAS, KRAS, MRAS, NRAS, RIT1,_ and _RRAS2._

Evidence considered

• The KRAS VCEP PS1 rule requires the same amino-acid change as a previously established pathogenic variant, regardless of nucleotide change, and applies to observed analogous positions in HRAS, KRAS, MRAS, NRAS, RIT1, and RRAS2.
• PMID:22722830 reports KRAS G12R in a Lim1215 cetuximab-resistance model and describes endogenous G12R knock-in, but does not establish a pathogenic clinical comparator variant.
• PMID:32792368 studies KRAS G12R in conditional mouse, cell, and organoid models, but provides no pathogenic alternate-nucleotide comparator.
• Alignment-with-PM1-domains.pptx.pdf was searched for c.34G>C, p.Gly12Arg, and p.G12R; no literal entry was found.

Still missing

• No literal c.34G>C, p.Gly12Arg, or p.G12R entry was found when Alignment-with-PM1-domains.pptx.pdf was searched.
• A previously established pathogenic KRAS p.G12R variant with a different nucleotide change is not documented in the available evidence.

Sources

Reasoning

The VCEP requires a de novo observation with the relevant parental confirmation and applies point-based strength adjustment. The available case evidence contains no proband-level de novo result, parental genotypes, maternity or paternity confirmation, or family-history information, so PS2 cannot be evaluated.

VCEP rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history; strength is assigned as Very Strong at 4 points, Strong at 2 points, or Moderate at 1 point.

Evidence considered

• No proband-level de novo observation, parental genotypes, maternity confirmation, paternity confirmation, or family-history result is reported in the available case evidence.

Still missing

• Documented de novo status in the proband
• Maternal genotype or confirmation
• Paternal genotype or confirmation
• Family-history information
• Phenotypic information needed for the VCEP point adjustment

Sources

Reasoning

The KRAS VCEP permits PS3 Supporting for one approved assay and PS3 Moderate for two or more different approved assays. The governing approved-functional-studies file was searched for c.34G>C, p.Gly12Arg, and p.G12R, with no exact variant entry. PMID:22722830 reports KRAS G12R activation and an endogenous knock-in resistance model, but its assay instance is not listed as an approved KRAS assay in the VCEP table. PMID:32792368 reports KRAS G12R in mouse models, MEFs, and organoids; the VCEP file states that animal models and variant-specific assays are excluded from the approved assay set, and this PMID is not listed under the approved KRAS RAS, MEK, or ERK assay instances. Therefore the available evidence does not establish one approved assay for this exact variant, so PS3 cannot be assigned under the VCEP rule.

VCEP rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Approved assays are available in the supplemental materials. ... One approved assay.

Evidence considered

• ClinGen RASopathy VCEP KRAS v2.3 rule: PS3 is applicable to well-established in vitro or in vivo functional studies, with approved assays available in the supplemental materials; one approved assay supports PS3 Supporting and two or more different approved assays support PS3 Moderate.
• SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx, READ ME and KRAS assay sections: approved KRAS RAS activation, MEK activation, and ERK activation assay instances are identified by their listed PMIDs; the table proposes PS3_Supporting and BS3_NA for those assay instances.
• The governing functional-studies text was searched for c.34G>C, p.Gly12Arg, and p.G12R; no exact variant entry was found.
• PMID:22722830, Results, AAV-mediated targeted homologous recombination; Fig. 2d,e: KRAS G12R was associated with increased KRAS activation, and endogenous G12R knock-in rendered Lim1215 cells resistant to cetuximab, but this publication is not a listed approved KRAS assay instance in the VCEP table.
• PMID:32792368, Results, Figure 2 paragraph: KRASG12R was studied in conditional mouse models, MEFs, pancreatic tissue, and organoids; this PMID is not a listed approved KRAS RAS, MEK, or ERK assay instance in the VCEP table.

Still missing

• No entry for c.34G>C, p.Gly12Arg, or p.G12R was found in SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx.txt.
• A qualifying exact-variant result from at least one KRAS VCEP-approved assay instance is not available in the reviewed evidence.

Sources

Reasoning

The KRAS VCEP makes PS4 applicable and requires significantly increased prevalence in affected individuals versus controls; its specified case-control route requires RR or OR >5.0 with a confidence interval that excludes 1.0, while the rare-variant alternative requires multiple unrelated patients with the same phenotype and absence in controls. The available evidence documents KRAS p.G12R in experimental cancer models and somatic oncology resources, but provides no extractable germline affected/control counts, matched-ancestry control comparison, RR/OR with 95% CI, or documented set of multiple unrelated RASopathy patients with the same phenotype. The literature_pass packet was checked: packet.ai_classified_papers contains only PMID:32792368 classified for PS3, not PS4; the PS4-indexed papers have no usable case-control or qualifying RASopathy phenotype data in the available extracts.

VCEP rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. ... Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence. ... ≥5 points. ... ≥3 points. ... ≥1 points.

Evidence considered

• The VCEP PS4 rule states that affected-individual prevalence must be significantly increased versus controls; its case-control note requires RR or OR >5.0 and a confidence interval that does not include 1.0, with a moderate rare-variant alternative based on multiple unrelated patients with the same phenotype and absence in controls.
• gnomAD v2.1 reports 0/249,272 alleles and gnomAD v4.1 reports the variant as absent, but no affected germline cohort count is available, so an OR and 95% CI cannot be computed.
• PMID:22722830 reports KRAS G12R in a Lim1215 colorectal cancer cell-line cetuximab-resistance model, not a germline phenotype case-control study.
• PMID:28572459 reports cohort-level enrichment of KRAS p.G12 mutations in GENIE versus TCGA but does not explicitly mention p.G12R and is a somatic cancer cohort comparison, not RASopathy prevalence evidence.
• PMID:24627688 is a lung-cancer ALK-testing guideline and does not provide a KRAS p.G12R case, phenotype, control comparison, or population-frequency analysis.
• PMID:32792368 studies KRAS G12R in conditional mouse and organoid models and reports no human case, segregation, or population-frequency data.

Still missing

• A germline case-control dataset or matched-ancestry control comparison with extractable counts is needed to calculate RR/OR and its 95% confidence interval.
• Alternatively, documented multiple unrelated RASopathy patients carrying KRAS p.Gly12Arg with the same phenotype and absence in controls are needed.

Sources

Reasoning

The KRAS VCEP PM5 rule requires one likely pathogenic residue change at the same codon for Moderate strength, or at least two different likely pathogenic residue changes at the same codon observed in at least five probands for Strong strength. The collected PM5 candidate evidence contains zero same-residue candidates, so the available evidence does not establish either threshold; no generic or non-VCEP comparator threshold was substituted.

VCEP rule

≥2 different [likely] pathogenic residues changes at the same codon observed in ≥5 probands. ... 1 [likely] pathogenic residue change at the same codon.

Evidence considered

• The KRAS VCEP PM5 rule assigns Moderate strength for 1 likely pathogenic residue change at the same codon and Strong strength for at least 2 different likely pathogenic residue changes at the same codon observed in at least 5 probands.
• The collected PM5 candidate summary reports 11 total candidates screened, 0 same-residue candidates, 0 expert-panel likely pathogenic candidates, and 0 non-expert-majority likely pathogenic candidates; this artifact is not used as a classification by itself.

Still missing

• A verified likely pathogenic alternate missense change at KRAS codon 12 is not documented in the available evidence.
• The required proband counts for any alternate codon-12 changes are unavailable.

Sources

Reasoning

The VCEP defines PM6 for an assumed de novo variant without confirmation of paternity and maternity and assigns strength from 0.5, 1, or 2 points. No assumed de novo observation or parental-testing information is available, so PM6 cannot be evaluated.

VCEP rule

Assumed de novo, but without confirmation of paternity and maternity; strength is assigned as Strong at 2 points, Moderate at 1 point, or Supporting at 0.5 points.

Evidence considered

• No assumed de novo observation, maternal result, paternal result, or other parental-testing information is reported in the available case evidence.

Still missing

• Evidence that the variant was assumed de novo
• Maternal genotype or confirmation
• Paternal genotype or confirmation
• Phenotypic information needed for the VCEP point adjustment

Sources

Reasoning

The VCEP evaluates PP1 by informative meioses, with Supporting at at least 3, Moderate at at least 5, and Strong at at least 7 informative meioses; segregation data for affected relatives are not available.

VCEP rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease; Supporting at ≥3 informative meioses, Moderate at ≥5, and Strong at ≥7.

Evidence considered

• No family pedigree, affected-relative testing, unaffected-relative testing, segregation result, or informative-meiosis count is reported in the available case evidence.

Still missing

• Affected relatives tested for the variant
• Unaffected relatives tested for the variant
• Pedigree relationships and phenotype data
• Count of informative meioses

Sources

Reasoning

The governing VCEP specifies BS2 using a point-based rule (−4 Points for strong or −1 Point for supporting), but the available population evidence reports zero observed alleles and zero homozygotes rather than any BS2 point assignment or qualifying control homozygote observations. The BS2 rule therefore cannot be evaluated without substituting an unstated generic rule.

VCEP rule

−4 Points. / −1 Point.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS specification v2.3, BS2 rules: −4 Points (strong) and −1 Point (supporting).
• gnomAD v2.1: exome AC=0, AN=249272, homozygotes=0; no qualifying control homozygote observation is reported.
• gnomAD v4.1: variant absent; no homozygote or point assignment is reported.
• gnomAD v2.1 non-cancer exome-only source: variant absent; no homozygote or point assignment is reported.

Still missing

• A VCEP-defined BS2 point assignment or qualifying homozygote observations in controls are unavailable.

Sources

Reasoning

The VCEP applies BS4 to lack of segregation in affected family members and requires only one informative meiosis. No affected-family-member testing, non-segregation result, or informative meiosis is available, and the VCEP caveats cannot be assessed.

VCEP rule

Lack of segregation in affected members of a family; requires only one informative meiosis.

Evidence considered

• No affected-family-member variant results, lack-of-segregation observation, pedigree, informative-meiosis count, phenocopy assessment, or assessment of another causal variant is reported in the available case evidence.

Still missing

• Affected family members and their phenotypes
• Variant testing results in affected family members
• Pedigree relationships
• At least one informative meiosis
• Assessment of phenocopy or multiple-causal-variant caveats

Sources

Reasoning

The KRAS VCEP BP2 rule requires an alternative molecular cause of a RASopathy in the same gene, with phenotype consistent with expected severity, and assigns strength from the VCEP point thresholds. The available evidence contains no documented second KRAS variant, pathogenic variant in cis or trans, phase determination, affected-proband observation, or alternate same-gene molecular cause; consequently, the required point total cannot be established.

VCEP rule

Points are awarded for an alternative molecular cause of a RASopathy in the same gene (and/or in conjunction with BP5) and the phenotype is consistent with expected severity of the RASopathy. ... ≥ (-1) Point.

Evidence considered

• ClinGen RASopathy Expert Panel KRAS Version 2.3 CSPEC entry: BP2 points are awarded for an alternative molecular cause of a RASopathy in the same gene and/or in conjunction with BP5 when phenotype is consistent with expected severity.
• No case evidence documents a second KRAS variant, pathogenic variant in cis or trans, phase, or an alternate same-gene molecular cause for this individual.

Still missing

• Documented alternate pathogenic or likely pathogenic KRAS variant in the same individual.
• Cis/trans phase determination for any second variant.
• Clinical phenotype and affected-proband documentation supporting the VCEP's BP2 point assignment.

Sources

Reasoning

The KRAS VCEP makes BP5 applicable when an alternative molecular cause of a RASopathy in a different gene, or a phenotype inconsistent with RASopathy fully explained by another causative variant, is present. No such alternative causative variant or qualifying phenotype is documented for this case, and no BP5 point total can be assigned. The VCEP's own point thresholds are ≥(-4) for Strong, ≥(-2) for Moderate, and ≥(-1) for Supporting; because the required case-specific points are unavailable, no threshold comparison is performed.

VCEP rule

Points are awarded for an alternative molecular cause of a RASopathy in a different gene (and/or in conjunction with BP2) and the phenotype is consistent with expected severity of the RASopathy. Points are also awarded for phenotypes inconsistent with a RASopathy and fully explained by a different causative variant (e.g. WES testing). ... ≥ (-4) Points. ... ≥ (-2) Points. ... ≥ (-1) Point.

Evidence considered

• The VCEP BP5 instructions require an alternative molecular cause of a RASopathy in a different gene with phenotype consistent with expected severity, or a phenotype inconsistent with RASopathy fully explained by a different causative variant.
• No alternative causative variant or qualifying discordant phenotype is documented in the available case evidence; therefore no BP5 points can be assigned and no numeric threshold inequality can be evaluated.

Still missing

• Documented alternative molecular cause in a different gene or a phenotype inconsistent with RASopathy fully explained by another causative variant is needed.
• The VCEP-specific BP5 point assignment for that evidence is needed before comparing with the applicable threshold.

Sources