KRAS c.34G>T, p.(Gly12Cys)

Reasoning

The KRAS RASopathy VCEP Version 2.3 framework specifies PS3 at Supporting strength for one approved assay. PMID:25705018 directly evaluated KRAS-G12C in isogenic MCF10A cells using a RAF1 RAS-binding-domain pulldown assay after EGF stimulation, with wild-type KRAS and other KRAS mutants as comparators; KRAS-G12C increased GTP-bound KRAS by up to approximately twofold, providing variant-specific evidence of increased RAS activation consistent with the established gain-of-function mechanism. PMID:16051643 independently studied the exact Ki-rasG12C allele in a doxycycline-inducible lung-specific mouse model and observed increased Ras/Ral signaling and downstream effector phosphorylation, but this additional in vivo context does not establish the VCEP's Moderate threshold of two or more different approved assays. Therefore PS3 is applied at Supporting strength, not Moderate.

Rule

KRAS RASopathy VCEP Version 2.3 PS3: Supporting for one approved assay; Moderate for two or more different approved assays.

Evidence considered

• The KRAS RASopathy VCEP Version 2.3 framework defines PS3 Supporting as one approved assay and PS3 Moderate as two or more different approved assays.
• PMID:25705018 used an isogenic MCF10A model with near-physiological KRAS expression and a RAF1 RAS-binding-domain pulldown assay after EGF stimulation; KRAS-G12C increased GTP-bound KRAS by up to approximately twofold compared with controls.
• PMID:16051643 used a doxycycline-inducible, lung-specific human Ki-rasG12C mouse model and reported increased Ras/Ral pathway activation and phosphorylation of downstream effectors, supporting the biological relevance of the gain-of-function result but not providing a second different approved assay for VCEP Moderate PS3.
• PMID:24256730 and PMID:26841430 provide additional exact-variant biochemical and cell-based functional context, but their nucleotide-exchange, effector-interaction, inhibitor-response, and downstream-signaling experiments do not establish two different approved assay categories under the KRAS VCEP PS3 rule.

Still missing

• A second different approved assay is not established from the available evidence, so the VCEP Moderate PS3 threshold is not met.

Sources

Reasoning

The governing KRAS VCEP specifies PM1 at Moderate strength for variants in its approved critical functional domains: P-loop amino acids 10-17, Switch I amino acids 25-40, Switch II amino acids 57-64, and SAK amino acids 145-156; it excludes specific amino-acid residues because those are handled by PM5. KRAS p.Gly12Cys affects residue 12, which lies within the approved P-loop domain. The vcep_materials domain_tables object is empty, so the governing framework's explicit domain list is used.

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 governing KRAS VCEP PM1 rule lists P-loop 10-17, Switch I 25-40, Switch II 57-64, and SAK 145-156 as applicable critical functional domains.
• The variant is NP_203524.1:p.(Gly12Cys), placing the altered residue at amino-acid position 12 within the approved P-loop interval 10-17.
• The VCEP rule states that PM1 is not applicable to specific amino-acid residues; residue 12 is assessed here as domain membership rather than as a residue-specific hotspot claim.

Sources

Reasoning

The governing KRAS VCEP specifies PM2 at Supporting strength when the variant is absent from controls in gnomAD. The variant is absent from gnomAD v4.1 and is observed at allele frequency 0 in gnomAD v2.1 all-comers exomes (0/249,272 alleles; 0 homozygotes) and in the available non-cancer exome subset (0/234,950 alleles; 0 homozygotes). This satisfies PM2 Supporting.

Rule

KRAS VCEP Version 2.3: PM2 Supporting when the variant is absent from controls (gnomAD).

Evidence considered

• The governing KRAS VCEP specifies PM2 at Supporting strength for a variant absent from controls in gnomAD.
• gnomAD v2.1 all-comers exomes report 0 alternate alleles among 249,272 alleles, allele frequency 0, and 0 homozygotes.
• The available gnomAD v2.1 non-cancer exome subset reports 0 alternate alleles among 234,950 alleles, allele frequency 0, and 0 homozygotes; gnomAD v4.1 reports the variant as absent.

Sources

Reasoning

The variant is missense, NM_033360.3:c.34G>T (p.Gly12Cys), so the applicable computational path is REVEL only; SpliceAI, BayesDel, and other splice predictions are not used for PP3. REVEL is 0.853, meeting the KRAS RASopathy VCEP Version 2.3 missense PP3 supporting threshold of >=0.7. The generic REVEL calibration also supports PP3 at supporting strength at >=0.644 (Pejaver et al. 2022, PMID:36413997), but the governing KRAS VCEP threshold takes precedence. The prediction is counted once and not reused for BP4 or BP7.

Rule

KRAS RASopathy VCEP Version 2.3: for missense variants, REVEL >=0.7 supports PP3.

Evidence considered

• The KRAS RASopathy VCEP Version 2.3 specifies PP3 supporting for missense variants at REVEL >=0.7.
• The case REVEL lookup reports a score of 0.853 for NM_033360.3:c.34G>T (p.Gly12Cys), which exceeds the governing threshold.
• The generic ClinGen SVI REVEL calibration gives a PP3 supporting threshold of >=0.644 (Pejaver et al. 2022, PMID:36413997); the KRAS VCEP threshold is controlling.

Sources

Reasoning

The KRAS VCEP framework defines PS4 at Supporting as >=1 point, Moderate as >=3 points, and Strong as >=5 points. The available exact-variant reports are somatic lung-cancer observations: PMID:11745231 found KRAS mutations in 40/106 lung adenocarcinomas, including 25 codon-12 cysteine substitutions, but did not establish a germline RASopathy case-control enrichment or an exact c.34G>T/p.Gly12Cys association; PMID:15696205 reported two exact p.G12C tumors among 60 refractory lung-cancer specimens without a matched-control comparison. Therefore no qualifying VCEP PS4 point score is established, and the evidence does not meet PS4 for this germline RASopathy assessment.

Rule

KRAS VCEP PS4: Supporting >=1 point; Moderate >=3 points; Strong >=5 points.

Evidence considered

• The KRAS VCEP framework states PS4 thresholds of >=1 point for Supporting, >=3 points for Moderate, and >=5 points for Strong.
• PMID:11745231 studied 106 primary lung adenocarcinomas and reported 40 K-ras-mutated tumors, including 25 codon-12 cysteine substitutions, but this is a somatic cancer cohort and not a germline RASopathy case-control analysis; the exact c.34G>T/p.Gly12Cys variant was not explicitly identified in the extraction.
• PMID:15696205 explicitly reported two p.G12C tumors among 60 refractory lung-cancer specimens, but provided no germline RASopathy case-control enrichment or VCEP point score.

Still missing

• No germline RASopathy case-control study or validated VCEP PS4 point assignment was identified for this exact variant.

Sources

Reasoning

The KRAS VCEP BA1 rule requires a gnomAD filtering allele frequency of at least 0.05%. The variant is absent from gnomAD v4.1 and has allele frequency 0 (0/249,272 alleles; 0 homozygotes) in gnomAD v2.1 all-comers exomes and 0 (0/234,950 alleles; 0 homozygotes) in the non-cancer exome subset. Therefore, the BA1 threshold is not reached.

Rule

KRAS VCEP Version 2.3: GnomAD filtering allele frequency ≥0.05%.

Evidence considered

• The governing KRAS VCEP specifies BA1 at a gnomAD filtering allele frequency of ≥0.05%.
• gnomAD v2.1 all-comers exomes report 0 alternate alleles among 249,272 alleles, allele frequency 0, and 0 homozygotes.
• The available gnomAD v2.1 non-cancer exome subset likewise reports 0 alternate alleles among 234,950 alleles, allele frequency 0, and 0 homozygotes; gnomAD v4.1 reports the variant as absent.

Sources

Reasoning

The KRAS VCEP BS1 rule requires a gnomAD filtering allele frequency of at least 0.025%. The variant is absent from gnomAD v4.1 and has allele frequency 0 (0/249,272 alleles) in gnomAD v2.1 all-comers exomes and 0 (0/234,950 alleles) in the non-cancer exome subset. The observed frequency does not reach the BS1 threshold.

Rule

KRAS VCEP Version 2.3: GnomAD filtering allele frequency ≥0.025%.

Evidence considered

• The governing KRAS VCEP specifies BS1 at a gnomAD filtering allele frequency of ≥0.025%.
• gnomAD v2.1 all-comers exomes report 0 alternate alleles among 249,272 alleles, allele frequency 0; the non-cancer exome subset reports 0 among 234,950 alleles, also allele frequency 0.
• gnomAD v4.1 reports the variant as absent.

Sources

Reasoning

The governing KRAS VCEP assigns BS2 based on its point-based rule, requiring benign-observation evidence in unaffected controls. Population data provide no such observation: gnomAD v2.1 all-comers exomes and the non-cancer exome subset both report 0 homozygotes, and gnomAD v4.1 reports the variant as absent. Thus BS2 is not met; absence of homozygotes is not evidence that the variant was observed in healthy adults.

Rule

KRAS VCEP Version 2.3: BS2 is assigned under the VCEP point-based benign-observation rule; no qualifying observation is present.

Evidence considered

• The governing KRAS VCEP BS2 rule uses a point-based benign-observation framework.
• gnomAD v2.1 all-comers exomes report 0 homozygotes, and the non-cancer exome subset also reports 0 homozygotes; gnomAD v4.1 reports the variant as absent.
• No unaffected-adult homozygote or other qualifying healthy-control observation is documented in the available population evidence.

Sources

Reasoning

The variant is missense, so BP4 must be assessed using REVEL only; the SpliceAI score is not substituted and BayesDel is not used because no applicable calibrated cutoff is established here. REVEL is 0.853, which does not meet the governing KRAS RASopathy VCEP Version 2.3 BP4 supporting threshold of <=0.3. Therefore BP4 is not met.

Rule

KRAS RASopathy VCEP Version 2.3: for missense variants, REVEL <=0.3 supports BP4.

Evidence considered

• The KRAS RASopathy VCEP Version 2.3 specifies BP4 supporting for missense variants at REVEL <=0.3.
• The case REVEL lookup reports a score of 0.853 for NM_033360.3:c.34G>T (p.Gly12Cys), exceeding the benign threshold.
• Because the variant is missense, its SpliceAI score is not evidence for BP4, and BayesDel is not used without a governing VCEP cutoff.

Sources

Reasoning

The KRAS VCEP specifies PS1 for the same amino-acid change as a previously established pathogenic variant, including analogous residue positions in HRAS, KRAS, MRAS, NRAS, RIT1, and RRAS2. The available evidence documents KRAS p.Gly12Cys itself, but does not establish a pathogenic alternate-nucleotide change encoding p.Gly12Cys or provide a clearly qualifying previously established pathogenic comparator. Therefore PS1 cannot be applied from the available evidence.

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.
• PMID:15696205 directly reports KRAS G12C in two lung-cancer specimens, but does not document a different nucleotide change encoding the same amino-acid substitution.
• PMID:25705018 directly studies KRAS-G12C alongside other KRAS variants, but does not establish an alternate-nucleotide p.Gly12Cys pathogenic comparator.

Still missing

• A validated pathogenic variant with a different nucleotide change encoding KRAS p.Gly12Cys is not documented.

Sources

Reasoning

The KRAS Version 2.3 framework specifies PS2 by de novo evidence points (Very Strong 4 points, Strong 2 points, Moderate 1 point), but the available case evidence contains no documented affected proband, confirmed maternity and paternity, parental testing, or de novo observation for NM_033360.3:c.34G>T (p.Gly12Cys). The available papers concern somatic cancer or experimental KRAS-G12C models and do not establish a germline de novo event.

Rule

KRAS Version 2.3: PS2 Very Strong at 4 points, Strong at 2 points, Moderate at 1 point.

Evidence considered

• The KRAS Version 2.3 framework assigns PS2 strengths of Very Strong at 4 points, Strong at 2 points, and Moderate at 1 point.
• No case-level trio, parental-testing, or confirmed de novo evidence for NM_033360.3:c.34G>T (p.Gly12Cys) is documented in the available evidence.
• The available variant papers describe somatic tumors or experimental models rather than a germline de novo observation.

Still missing

• Affected proband phenotype and clinical diagnosis
• Confirmed maternity and paternity
• Testing results for both biological parents
• Evidence that the variant is absent from both parents

Sources

Reasoning

The governing KRAS VCEP PM5 rule permits Moderate strength for one pathogenic or likely pathogenic residue change at the same codon and Strong strength for at least two such changes observed in at least five probands. The collected PM5 search returned 11 candidates but no same-residue candidates, and the retrieval recorded an HTTP 429 failure; the available paper extracts document KRAS codon-12 variants but do not establish a qualifying alternate pathogenic or likely pathogenic residue change at codon 12 under the VCEP rule. The evidence is therefore insufficient to conclude that PM5 is absent or met.

Rule

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

Evidence considered

• The governing KRAS VCEP PM5 rule requires one pathogenic or likely pathogenic residue change at the same codon for Moderate strength, or at least two such changes observed in at least five probands for Strong strength.
• The collected comparator artifact reports 11 total candidates but zero same-residue candidates, with an HTTP 429 retrieval error; this soft failure prevents treating the empty candidate list as a definitive negative result.
• PMID:11745231 reports codon-12 GGT-to-TGT p.Gly12Cys observations but does not establish an alternate codon-12 residue change meeting the VCEP PM5 requirements.
• PMID:25705018 studies KRAS G12D, G12V, G12C and other variants, but the extracted evidence does not establish a qualifying pathogenic or likely pathogenic alternate residue change at codon 12 with the required proband evidence.

Still missing

• A validated search of KRAS codon-12 alternate missense variants with pathogenic or likely pathogenic status and proband evidence is still required.

Sources

Reasoning

The KRAS Version 2.3 framework specifies PM6 using 2 points for Strong, 1 point for Moderate, and 0.5 points for Supporting evidence, but no presumed de novo occurrence without confirmed parental testing is documented for NM_033360.3:c.34G>T (p.Gly12Cys). The available literature is somatic or experimental and provides no affected proband-parent observation from which PM6 points can be assigned.

Rule

KRAS Version 2.3: PM6 Strong at 2 points, Moderate at 1 point, Supporting at 0.5 points.

Evidence considered

• The KRAS Version 2.3 framework assigns PM6 strengths of Strong at 2 points, Moderate at 1 point, and Supporting at 0.5 points.
• No presumed de novo case without parental testing is documented in the available case evidence.
• The available publications describe somatic cancer findings or laboratory models and do not provide PM6-eligible clinical observations.

Still missing

• Affected proband phenotype and clinical diagnosis
• A case report or cohort record documenting this variant in an affected proband
• Evidence that parental testing was unavailable or incomplete

Sources

Reasoning

The KRAS Version 2.3 framework defines PP1 as Supporting for at least 3 informative meioses, Moderate for at least 5, and Strong for at least 7. No affected relatives, variant-positive relatives, phenotype concordance, pedigree, or informative meioses are documented for NM_033360.3:c.34G>T (p.Gly12Cys), so no segregation strength can be assigned.

Rule

KRAS Version 2.3: PP1 Supporting at >=3 informative meioses, Moderate at >=5, Strong at >=7.

Evidence considered

• The KRAS Version 2.3 framework defines PP1 as Supporting at 3 or more informative meioses, Moderate at 5 or more, and Strong at 7 or more.
• No family segregation data, affected relatives, or informative meioses are documented in the available case evidence.

Still missing

• Pedigree and affected-relative information
• Genotypes of informative relatives
• Phenotype status of relatives
• Count of informative meioses

Sources

Reasoning

The KRAS Version 2.3 framework requires only one informative meiosis for BS4, but no informative unaffected relative, non-segregation observation, family genotype, or phenotype assessment is documented for NM_033360.3:c.34G>T (p.Gly12Cys). The available somatic and experimental publications do not provide BS4-eligible family evidence.

Rule

KRAS Version 2.3: BS4 Strong requires only one informative meiosis.

Evidence considered

• The KRAS Version 2.3 framework states that BS4 requires one informative meiosis.
• No non-segregation, unaffected-relative, or informative family data are documented in the available case evidence.

Still missing

• Informative unaffected relatives
• Relative genotypes
• Phenotype assessments and age-related penetrance information
• Documented non-segregation meiosis

Sources

Reasoning

The governing KRAS Version 2.3 framework permits BP2 at supporting, moderate, or strong strength according to its point-based rules, but the available case evidence contains no affected-proband observation documenting a second pathogenic or likely pathogenic variant in cis or trans with KRAS c.34G>T (p.Gly12Cys). The cited literature concerns somatic or functional KRAS G12C observations and does not establish allelic phase or a clinically relevant second variant. Therefore BP2 cannot be applied or excluded from the available evidence.

Rule

Apply BP2 only when the relevant second pathogenic variant and its cis/trans relationship are documented under the KRAS Version 2.3 point-based framework; those data are absent here.

Evidence considered

• The governing KRAS Version 2.3 framework defines BP2 as a point-based benign criterion with supporting, moderate, and strong options, but it does not provide case-specific BP2 points here.
• The reviewed literature reports KRAS G12C in lung tumors or experimental models, without documenting a second pathogenic variant or cis/trans phase in an affected proband.
• PMID:11745231 reports tumor KRAS codon 12 mutation observations, PMID:15696205 reports two KRAS G12C lung tumor specimens, and PMID:16051643 studies a Ki-rasG12C mouse model; none establishes the allelic observations required for BP2.

Still missing

• No clinical case-level evidence identifies a second pathogenic or likely pathogenic variant in the same individual.
• No phasing information establishes cis or trans configuration for any second variant.

Sources

Reasoning

The KRAS VCEP defines BP5 using a point score with the criterion-specific direction written as >= (-1) Point for Supporting, >= (-2) Points for Moderate, and >= (-4) Points for Strong. No validated BP5 point score or qualifying benign alternative-molecular-diagnosis evidence is available for this case, so the required inequality cannot be evaluated: point score >= (-1)? not available. The rule is therefore not assessed rather than inferred from unrelated evidence.

Rule

KRAS VCEP BP5: >= (-1) Point Supporting; >= (-2) Points Moderate; >= (-4) Points Strong.

Evidence considered

• The KRAS VCEP writes BP5 thresholds as >= (-4) Points for Strong, >= (-2) Points for Moderate, and >= (-1) Point for Supporting.
• No case-specific BP5 point score or qualifying benign alternative-molecular-diagnosis evidence was identified; therefore the explicit comparison 'point score >= (-1)?' cannot be completed.

Still missing

• A validated KRAS VCEP BP5 point score and qualifying evidence for an alternative molecular diagnosis are unavailable.

Sources