HRAS c.35G>T, p.Gly12Val

Reasoning

The variant is HRAS NM_005343.4:c.35G>T, p.(Gly12Val)/p.(G12V). ClinVar variation 12600 records this exact variant as Pathogenic with multiple submitters and no conflicts, establishing the same amino acid change required by the HRAS VCEP PS1 rule. The VCEP rule applies to observed analogous residue positions in HRAS and the other named RASopathy genes. The governing HRAS PM1 alignment file was searched for c.35G>T, p.Gly12Val, and p.G12V; no exact variant notation was found there, but that file is not needed to establish PS1.

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

• ClinGen RASopathy Expert Panel HRAS v2.3 PS1 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.
• ClinVar variation 12600: NM_005343.4:c.35G>T (p.Gly12Val) is classified Pathogenic, with review status 'criteria provided, multiple submitters, no conflicts' and 10 clinical laboratories.

Still missing

• No c.35G>T, p.Gly12Val, or p.G12V entry was found when searching Alignment-with-PM1-domains.pptx.pdf.txt; this PM1 file is not required for PS1.

Sources

Reasoning

The exact HRAS NM_005343.4:c.35G>T (p.Gly12Val) record documents a Costello syndrome proband in whom the variant was verified de novo in Aoki et al. (PMID:16170316). A separate clinical submission describes the variant as recurrently de novo in multiple individuals, but the available evidence does not provide a complete case-by-case count or parental-testing details needed to justify a higher point tier. The VCEP PS2 rule assigns Moderate strength at 2 points; the verified de novo proband supports that tier, subject to human confirmation of the primary report.

VCEP rule

2 Points.

Evidence considered

• ClinVar submission audit, SCV000062137: exact-variant clinical submission states that the Gly12Val variant was reported in a Costello syndrome proband and verified to have occurred de novo in that individual, citing Aoki 2005.
• ClinVar submission audit, SCV004072496: exact-variant clinical submission states that the variant was observed or determined to result from a de novo mutation in multiple individuals with features consistent with HRAS-related RASopathy.
• Aoki et al. 2005, PMID:16170316, Germline mutations in HRAS proto-oncogene cause Costello syndrome: cited by the validated submission as the source of the verified de novo proband observation.
• ClinGen RASopathy Expert Panel HRAS V2.3 CSPEC PS2 rule: 2 Points.

Still missing

• The primary report's case-level parental testing, phenotype details, and the total number of qualifying de novo probands were not available in the extracted case materials.

Sources

Reasoning

The HRAS c.35G>T (p.Gly12Val/p.G12V) variant is explicitly listed as a pathogenic or likely pathogenic validation control (G12V - P or P/LP) in three approved HRAS pathway assay types: RAS activation, MEK activation, and ERK activation. The VCEP functional-studies table marks each assay approved and assigns PS3_Supporting, while the VCEP rule states that two or more different approved assays support Moderate strength. Therefore PS3 is met at Moderate strength. No benign functional result is reported for this variant.

VCEP rule

Two or more different approved assays. ... Two or more unique assay types (i.e. RAS activation assay and MEK activation assay) for a given variant provides sufficient evidence to upgrade PS3 to the Moderate strength.

Evidence considered

• SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx, RAS Activation Assay sheet, HRAS column: G12V is listed among 10 P/LP validation controls as "G12V - P"; the assay is approved (Y) and its proposed strength is PS3_Supporting; BS3_NA.
• SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx, MEK Activation Assay sheet, HRAS column: G12V is listed among four P/LP validation controls as "G12V - P/LP"; the assay is approved (Y) and its proposed strength is PS3_Supporting; BS3_NA.
• SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx, ERK Activation Assay sheet, HRAS column: G12V is listed among 12 P/LP validation controls as "G12V - P"; the assay is approved (Y) and its proposed strength is PS3_Supporting; BS3_NA.
• The table's READ ME states: "Two or more unique assay types (i.e. RAS activation assay and MEK activation assay) for a given variant provides sufficient evidence to upgrade PS3 to the Moderate strength."

Sources

Reasoning

The variant changes HRAS residue 12. The HRAS VCEP PM1 specification limits PM1 to the listed critical functional domains, including the P-loop at amino acids 10-17; residue 12 is within that domain. The governing alignment file was consulted through its extracted table, which identifies the HRAS P-loop as residues 10-17. The authoritative domain_tables key is present but empty, so no additional gene-specific domain table supersedes the CSPEC supplementary domain list. The alignment file was searched for c.35G>T, p.Gly12Val, and p.G12V; no exact variant notation was found, but the residue mapping is sufficient.

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

• ClinGen RASopathy Expert Panel HRAS v2.3 PM1 rule: PM1 is applicable only to critical and well-established functional domains in the supplementary table, including P-loop [AA 10-17], SW1 [AA 25-40], SW2 [AA 57-64], and SAK [AA 145-156].
• Alignment-with-PM1-domains.pptx.pdf, Page 1 table: HRAS P-loop is listed as residues 10-17; the variant's altered residue is Gly12, within this region.
• Variant normalization: NM_005343.4:c.35G>T produces NP_005334.1:p.(Gly12Val)/p.(G12V).

Still missing

• No c.35G>T, p.Gly12Val, or p.G12V entry was found when searching Alignment-with-PM1-domains.pptx.pdf.txt; the file provides the domain alignment rather than variant-level records.

Sources

Reasoning

The HRAS NM_005343.4:c.35G>T (p.Gly12Val) variant is absent from gnomAD v2.1 and gnomAD v4.1. The non-cancer subsets also report absence, and no population allele frequency or homozygote is reported. This satisfies the VCEP PM2 rule at Supporting strength.

VCEP rule

The variant must be absent from controls (gnomAD).

Evidence considered

• gnomAD v2.1 (GRCh37, query 11-534288-C-A): variant absent; no allele-frequency record or homozygote reported.
• gnomAD v4.1 (GRCh38, query 11-534288-C-A): variant absent; no allele-frequency record or homozygote reported.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also reported the variant absent.
• ClinGen RASopathy Expert Panel HRAS v2.3 CSPEC entry for PM2: The variant must be absent from controls (gnomAD).

Sources

Reasoning

The exact-variant clinical submission SCV007593551 describes the variant as likely de novo in the current proband, with the possibility of parental germline mosaicism not excluded, and labels this evidence PS2_Moderate. This is assumed rather than verified de novo evidence and is therefore relevant to PM6, but the submission does not provide the proband's full phenotype or parental test results. The VCEP PM6 rule assigns Moderate strength at 1 point; the documented likely-de-novo proband supports that tier, pending confirmation from the underlying clinical report.

VCEP rule

1 Point.

Evidence considered

• ClinVar submission audit, SCV007593551: exact-variant submission states that the variant likely occurred de novo in the current proband, while parental germline mosaicism could not be excluded, and records PS2_Moderate.
• ClinVar submission audit, SCV004114489: exact-variant submission describes the variant as recurrently de novo in multiple individuals with Costello syndrome, but its cited PMID trail was not validated in this case.
• The VCEP PM6 rule assigns Moderate strength at 1 Point.

Still missing

• The underlying clinical report and detailed parental-testing results for the assumed de novo observation were not available.

Sources

Reasoning

Scope: the HRAS VCEP applies PP3 to missense variants using REVEL ≥ 0.7, and separately allows a splicing-impact path when the predicted outcome matches the disease mechanism. This variant is missense (NM_005343.4:c.35G>T; p.Gly12Val), so the named missense predictor applies. The REVEL score is 0.789, exceeding the VCEP cutoff of 0.7; therefore PP3 is met at supporting strength. The REVEL result is sufficient for PP3 and the SpliceAI result is not additionally counted.

VCEP rule

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

Evidence considered

• ClinGen RASopathy Expert Panel HRAS v2.3 criterion entry: PP3 missense path requires REVEL ≥ 0.7.
• Local REVEL predictor lookup for NM_005343.4:c.35G>T: REVEL score = 0.789, which exceeds 0.7.

Sources

Reasoning

The HRAS NM_005343.4:c.35G>T (p.Gly12Val) variant is absent from gnomAD v2.1 and gnomAD v4.1, with no reported allele frequency. Therefore, the VCEP BA1 threshold is not reached.

VCEP rule

GnomAD filtering allele frequency ≥0.05%.

Evidence considered

• gnomAD v2.1 (GRCh37, query 11-534288-C-A): variant absent; no allele-frequency record.
• gnomAD v4.1 (GRCh38, query 11-534288-C-A): variant absent; no allele-frequency record.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also reported the variant absent.
• ClinGen RASopathy Expert Panel HRAS v2.3 CSPEC entry for BA1: GnomAD filtering allele frequency ≥0.05%.

Sources

Reasoning

The HRAS NM_005343.4:c.35G>T (p.Gly12Val) variant is absent from gnomAD v2.1 and gnomAD v4.1, with no reported allele frequency. Therefore, the VCEP BS1 threshold is not reached.

VCEP rule

GnomAD filtering allele frequency ≥0.025%.

Evidence considered

• gnomAD v2.1 (GRCh37, query 11-534288-C-A): variant absent; no allele-frequency record.
• gnomAD v4.1 (GRCh38, query 11-534288-C-A): variant absent; no allele-frequency record.
• gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also reported the variant absent.
• ClinGen RASopathy Expert Panel HRAS v2.3 CSPEC entry for BS1: GnomAD filtering allele frequency ≥0.025%.

Sources

Reasoning

Scope: the HRAS VCEP applies BP4 to missense variants using REVEL ≤ 0.3. This variant is missense, so BP4 is applicable, but its REVEL score is 0.789, which is above rather than at or below the VCEP cutoff. The SpliceAI no-impact result is not used to establish BP4 because the VCEP's BP4 rule names REVEL for missense variants and does not provide a splice-prediction path.

VCEP rule

For missense variants: REVEL ≤0.3.

Evidence considered

• ClinGen RASopathy Expert Panel HRAS v2.3 criterion entry: BP4 missense path requires REVEL ≤ 0.3.
• Local REVEL predictor lookup for NM_005343.4:c.35G>T: REVEL score = 0.789, which does not meet the ≤0.3 cutoff.

Sources

Reasoning

The HRAS VCEP applies PS4 using point-based scoring for autosomal-dominant cases with phenotypic specifications, with strong, moderate, and supporting levels requiring ≥5, ≥3, and ≥1 points, respectively. The available case packet does not provide a verified PS4 point assignment, affected/unaffected control counts, a case-control estimate, or a verified paper finding establishing the required phenotype-specific proband evidence. The literature packet indexes papers as PS4 candidates, but the only AI-classified paper is classified for PM1 rather than PS4 and has no abstract or paper_extracts entry available for verification; the locally fetched publications contain no corresponding full-text record. Therefore PS4 cannot be assigned from the available evidence without substituting unverified literature or a generic rule.

VCEP rule

Strength adjustment using point-based scoring for autosomal dominant cases with phenotypic specifications: full points awarded with RASopathy phenotypes, reduced points applicable to cases with minimal phenotypic information (i.e. prenatal cases, cases with a clinical order of a RASopathy panel without clinical information, and cases with limited clinical information in other global tests (such as WES)). ... ≥5 points. ... ≥3 points. ... ≥1 points.

Evidence considered

• ClinGen RASopathy Expert Panel HRAS v2.3 PS4 criterion: strength is adjusted using point-based scoring for autosomal-dominant cases with phenotypic specifications.
• ClinGen RASopathy Expert Panel HRAS v2.3 PS4 strength thresholds: strong ≥5 points, moderate ≥3 points, supporting ≥1 point.
• The literature packet lists PS4 candidate PMIDs, but no verified abstract/full-text finding or extracted affected/control counts are available for this case; the single ai_classified_papers entry is classified for PM1, not PS4.

Still missing

• Verified PS4 evidence from affected and control counts or a VCEP-compatible point-based proband assessment is missing.
• The PS4-indexed literature candidates lack an available abstract/full-text extraction sufficient for independent verification.

Sources

Reasoning

The HRAS VCEP PM5 rule requires at least 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 available PM5 candidate collection contains zero same-residue candidates, and paper_extracts.json contains no extracted paper findings. No qualifying comparator evidence can therefore be confirmed from the available evidence.

VCEP rule

1 [likely] pathogenic residue change at the same codon.

Evidence considered

• ClinGen RASopathy Expert Panel HRAS v2.3 PM5 rule: 1 likely pathogenic residue change at the same codon supports Moderate, while at least 2 different likely pathogenic residue changes at the same codon observed in at least 5 probands supports Strong.
• pm5_candidates.json: classic_same_residue_missense mode; total_candidates_seen = 0, same_residue_candidates = 0, and no useful candidates found.

Still missing

• A confirmed likely pathogenic HRAS missense change at codon 12, with the evidence needed to establish its qualification under the VCEP PM5 rule, is unavailable.
• The PM5 candidate collection reports zero same-residue candidates and a retrieval error; paper_extracts.json is empty.

Sources

Reasoning

No documented affected or unaffected relatives, informative meioses, or family-level segregation results are available for this exact variant. The VCEP PP1 thresholds require a count of informative meioses, so PP1 cannot be evaluated.

Still missing

• Affected-relative and unaffected-relative genotypes with phenotype status.
• The number of informative meioses.

Reasoning

No evidence is available showing this variant in a healthy homozygous or heterozygous individual, nor are there phenotype-specific points for an unaffected carrier or a parent/sibling sample. The VCEP's point-based BS2 assessment therefore cannot be performed.

VCEP rule

Strength adjustment using point-based scoring based on phenotypic specifications. Phenotypic specifications: based on healthy homozygote or heterozygote individuals, reduced points for apparently unaffected heterozygous individuals, applicable to parent or sibling samples during clinical family evaluations.

Evidence considered

• The available gnomAD records establish absence, not observation in a healthy homozygous or heterozygous individual and not the phenotype-specific point value required by the VCEP.
• ClinGen RASopathy Expert Panel HRAS v2.3 CSPEC entry for BS2 requires point-based scoring based on healthy homozygote or heterozygote individuals, with reduced points for apparently unaffected heterozygous individuals and applicability to parent or sibling samples during clinical family evaluations; its applicable strength rules are -4 Points and -1 Point.

Still missing

• Healthy individual genotype and phenotype data, including zygosity and family-sample context, are unavailable for VCEP BS2 point scoring.

Sources

Reasoning

No non-segregation observation is documented: the available record does not identify an informative unaffected relative who carries the exact variant or an affected relative who lacks it. The VCEP BS4 rule requires one informative meiosis, so BS4 cannot be evaluated.

Still missing

• A documented informative meiosis showing non-segregation, including relative phenotype and genotype.

Reasoning

The HRAS VCEP Version 2.3 entry provides BP2 strength mappings of Strong for ≥ (-4) points, Moderate for ≥ (-2) points, and Supporting for ≥ (-1) point. The available case evidence does not document phase, a second variant, or a qualifying cis/trans allelic observation from affected probands; therefore, the VCEP point total cannot be determined and BP2 is not assessed.

VCEP rule

≥ (-1) Point.

Evidence considered

• ClinGen RASopathy Expert Panel HRAS Version 2.3 CSPEC criterion entry: BP2 is Supporting at ≥ (-1) point, Moderate at ≥ (-2) points, and Strong at ≥ (-4) points.
• No case-level record in the reviewed evidence documents phase, a second allele, or a qualifying cis/trans observation in affected probands.

Still missing

• Documented cis/trans phase and the relevant second allele or variant observation are needed to calculate the VCEP BP2 point total.

Sources

Reasoning

The HRAS VCEP applies BP5 when an alternative molecular cause of a RASopathy is present in a different gene, with the phenotype consistent with the expected RASopathy severity, or when an inconsistent phenotype is fully explained by a different causative variant. The available evidence does not document an alternative causative variant, its gene, a phenotype fully explained by that variant, or a VCEP BP5 point total. Consequently BP5 cannot be assessed; no generic alternative-cause rule is substituted.

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). ... ≥ (-1) Point.

Evidence considered

• ClinGen RASopathy Expert Panel HRAS v2.3 BP5 instructions: points require an alternative molecular cause in a different gene and a compatible or fully explained phenotype.
• No qualifying alternative causative variant, phenotype explanation, or BP5 point assignment is present in the available case evidence.

Still missing

• Documented alternative molecular cause in a different gene and phenotype relationship is missing.
• A VCEP BP5 point total is missing.

Sources