ERBB3 c.310G>A, p.Val104Met

Reasoning

PS3 is met at strong strength. Jaiswal et al. directly tested ERBB3 p.Val104Met in multiple orthogonal functional systems. In BaF3 cells, p.Val104Met promoted approximately 10- to 300-fold interleukin-3-independent survival when co-expressed with ERBB2, increased colony formation and downstream pERBB3/pERBB2/pAKT/pERK signaling, and required kinase-active ERBB2; empty-vector, ERBB3 wild-type, and kinase-dead ERBB2 controls were included. The variant also increased anchorage-independent growth, signaling, proliferation, and abnormal acinar structures in epithelial models, and ERBB3-mutant/ERBB2 cells produced accelerated in vivo tumor or leukemia-like growth, while ERBB3 knockdown reduced growth. These are variant-specific, biologically relevant, concordant cellular and in vivo results with appropriate negative and mechanistic controls, supporting a damaging gain-of-function effect.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Jaiswal et al. 2013, Figure 5A-C: ERBB3 V104M was tested in BaF3 cells with ERBB2; unlike ERBB3-WT, the mutant promoted approximately 10- to 300-fold IL-3-independent survival, increased colony formation, and increased downstream signaling.
• Jaiswal et al. 2013, Figures 2-3: ERBB3 V104M with ERBB2 increased anchorage-independent growth, phospho-ERBB3/phospho-ERBB2/phospho-AKT/phospho-ERK signaling, epithelial-cell proliferation, and abnormal acinar structures relative to ERBB3-WT/ERBB2 controls.
• Jaiswal et al. 2013, Figures 2E and 6: ERBB3-mutant/ERBB2 cells, including V104M in the epithelial model, promoted in vivo tumor or leukemia-like growth; empty-vector and ERBB3-WT controls were included.
• Jaiswal et al. 2013, Figure 5A-F: loss of activity with kinase-dead ERBB2 and lack of comparable activity from ERBB3-WT or mutant ERBB3 alone provided mechanistic and negative controls.
• Ng et al. 2018, Results, High-Sensitivity Functional Mutation Annotation: ERBB3V104M is described as activating signaling and inducing cell survival when co-expressed with wild-type ERBB2, consistent with the primary study's functional findings.

Sources

Reasoning

ERBB3 p.Val104Met is reported in Cancer Hotspots as lying in a statistically significant hotspot at residue V104. No ERBB3 VCEP or gene-specific domain table is present, so generic ACMG/AMP PM1 applies; the variant is also extremely rare in gnomAD v4.1 (AF 6.19542e-07; 1/1,614,096 alleles; no homozygotes), providing no common-population benign signal for the observed hotspot variant. The hotspot extraction is flagged as partial and should be confirmed against the stored screenshot before final clinical sign-off.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• Cancer Hotspots query ERBB3 V104 reports that the variant lies in a statistically significant hotspot; the extraction warning states that the V104 row was only partially parsed.
• gnomAD v4.1 reports ERBB3 p.Val104Met at total AF 6.19542e-07, 1 of 1,614,096 alleles, with zero homozygotes.

Still missing

• The Cancer Hotspots row was only partially parsed and should be visually confirmed from the stored screenshot.

Sources

Reasoning

PM2 is met at supporting strength. The generic supporting threshold supplied for this case is <= 0.0001. The variant is absent from gnomAD v2.1 and from the reported gnomAD v2.1 and v3.1 non-cancer datasets; in gnomAD v4.1 it is present only once among 1,614,096 alleles (AF 6.19542e-07) with zero homozygotes. This is an extremely low population frequency and is below the PM2 supporting threshold.

Rule

PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1: absent.
• gnomAD v2.1 non-cancer: absent; gnomAD v3.1 non-cancer: absent, as reported in the case evidence.
• gnomAD v4.1: total AC=1, AN=1,614,096, AF=6.195418364211298e-07, total homozygotes=0.
• The generic PM2 supporting threshold supplied for this case is <= 0.0001; 6.195418364211298e-07 is below that threshold.

Still missing

• The case's source registry does not provide separate citation keys for the non-cancer gnomAD subsets
• gnomAD v4.1 grpmax FAF was not reported

Sources

Reasoning

NM_001982.4:c.310G>A is a missense variant, p.(Val104Met), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3 in this situation. REVEL is 0.584, below the generic ClinGen SVI supporting PP3 threshold of >=0.644 (Pejaver et al. 2022, PMID:36413997), and therefore does not meet PP3 at any strength.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• Variant consequence is missense: NM_001982.4:c.310G>A, NP_001973.2:p.(Val104Met), exon 3.
• REVEL score = 0.584; the supplied generic ClinGen SVI calibration sets PP3 supporting at >=0.644, moderate at >=0.773, and strong at >=0.932 (Pejaver et al. 2022, PMID:36413997).
• SpliceAI max delta = 0.004 was not counted because the governing generic path for a missense variant is REVEL only; BayesDel was not counted because no generic ACMG-strength calibration is established.

Sources

Reasoning

PP5 is not met because the exact-variant ClinVar record has no expert-panel submission. ClinVar variation 376410 exactly matches NM_001982.4:c.310G>A (p.Val104Met), but the audit reports expert_panel_submissions=0, criterion_lead_submissions=0, and only a non-expert somatic submission. The ClinVar record's Pathogenic classification, OncoKB's variant-specific Oncogenic label, and PMID:29533785's functional discussion are not exact-variant ClinVar expert-panel classifications and cannot trigger PP5 under the specified rule.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 376410 exactly matches NM_001982.4:c.310G>A (p.Val104Met), but the audit reports expert_panel_submissions=0 and criterion_lead_submissions=0.
• The available ClinVar submission is SCV004040593, a somatic research submission classified Pathogenic with no assertion criteria and no expert-panel status.
• PMID:29533785 states that ERBB3V104M is oncogenic in OncoKB based on prior functional work; this is not an exact-variant ClinVar expert-panel classification.

Sources

Reasoning

BA1 is not met. The default stand-alone threshold is >= 0.05. gnomAD v4.1 reports 1/1,614,096 total alleles (AF 6.19542e-07; homozygotes 0), with the highest population point estimate in European non-Finnish individuals at 1/1,180,020 alleles (8.47443e-07). The reported grpmax FAF is unavailable, but the observed frequency is already many orders of magnitude below 5%; there is no population-frequency basis for a stand-alone benign call.

Rule

BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)

Evidence considered

• gnomAD v4.1: total AC=1, AN=1,614,096, AF=6.195418364211298e-07, total homozygotes=0; highest observed population was European (non-Finnish), AC=1, AN=1,180,020, AF=8.47443263673497e-07.
• The generic BA1 default supplied for this case is >= 0.05; the observed gnomAD frequency is far below that threshold.

Still missing

• gnomAD v4.1 grpmax FAF was not reported

Sources

Reasoning

BS1 is not met. The generic default threshold is >= 0.01, while gnomAD v4.1 reports AF 6.19542e-07 overall and 8.47443e-07 in the highest observed population. These values are far below 1%, so the allele is not more frequent than expected on the supplied population-frequency evidence. The grpmax FAF is unavailable, but this does not alter the conclusion because even the observed point estimates are far below the default threshold.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v4.1: total AF=6.195418364211298e-07 from 1/1,614,096 alleles; highest population point estimate AF=8.47443263673497e-07 in European (non-Finnish) individuals.
• The generic BS1 default supplied for this case is >= 0.01; both reported frequencies are far below it, so a maximum-credible-frequency calculation is not outcome-determinative here.
• The reported grpmax FAF is null; no popmax point estimate was used as a substitute for FAF.

Still missing

• No gene- or disorder-specific maximum credible allele frequency calculation was available

Sources

Reasoning

BS3 is not met because the available variant-specific functional evidence does not show no damaging effect. Instead, Jaiswal et al. reported that ERBB3 p.Val104Met increased ERBB2-dependent signaling, cellular transformation and survival, and in vivo tumorigenic activity compared with ERBB3 wild-type and control constructs. No well-established assay demonstrating preserved protein function or normal splicing for p.Val104Met was identified.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• Jaiswal et al. 2013, Figures 2-6: variant-specific assays showed increased signaling, transformation, cell survival, and in vivo growth for ERBB3 V104M in the appropriate ERBB2-dependent context, contradicting a benign functional interpretation.
• No normal-function or normal-splicing assay for ERBB3 p.Val104Met was reported in the reviewed variant-specific studies.

Still missing

• No well-established variant-specific assay demonstrated a lack of damaging effect on ERBB3 protein function or splicing.

Sources

Reasoning

NM_001982.4:c.310G>A is a missense variant, p.(Val104Met), so the governing generic rule selects the REVEL path only; a no-impact SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.584, above the generic ClinGen SVI supporting BP4 threshold of <=0.29 (Pejaver et al. 2022, PMID:36413997), so BP4 is not met. BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)

Evidence considered

• Variant consequence is missense: NM_001982.4:c.310G>A, NP_001973.2:p.(Val104Met), exon 3.
• REVEL score = 0.584; the supplied generic ClinGen SVI calibration sets BP4 supporting at <=0.29, moderate at <=0.183, and strong at <=0.016 (Pejaver et al. 2022, PMID:36413997).
• SpliceAI max delta = 0.004 was not counted because SpliceAI is not the applicable path for a missense variant; a gray-zone REVEL result does not permit substituting SpliceAI.

Sources

Reasoning

BP6 is not met because the exact-variant ClinVar record has no expert-panel submission reporting the variant as benign or likely benign. ClinVar variation 376410 has a non-expert somatic Pathogenic submission and no expert-panel submissions; no qualifying exact-variant ClinVar benign or likely-benign expert-panel assertion is present.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 376410 exactly matches NM_001982.4:c.310G>A (p.Val104Met), but the submission audit reports expert_panel_submissions=0.
• The available ClinVar submission is somatic and Pathogenic, not benign or likely benign, and has no assertion criteria.

Sources

Reasoning

The variant is ERBB3 NP_001973.2:p.(Val104Met), but the available evidence does not establish a previously established pathogenic variant with the same amino-acid change caused by a different nucleotide change. The ClinVar record is a somatic, zero-star record without usable assertion criteria, and the literature evidence identifies this same variant as oncogenic rather than documenting an independent prior pathogenic observation suitable for PS1.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinVar variation 376410 exactly matches NM_001982.4:c.310G>A (p.Val104Met), but the available record has no assertion criteria, no expert-panel review, and a somatic origin.
• Ng et al. 2018 explicitly mentions ERBB3V104M and describes it as oncogenic in OncoKB based on prior signaling and cell-survival findings; this is not an independent same-amino-acid/different-nucleotide pathogenic observation.

Still missing

• A validated clinical or expert-panel record for an independently observed ERBB3 Val104Met variant caused by a different nucleotide change is needed.

Sources

Reasoning

PS2 cannot be assessed because the available case records do not document a proband with the relevant disease phenotype, absence of family history, or confirmed maternity and paternity for NM_001982.4:c.310G>A. The available variant-specific records instead describe ERBB3 p.Val104Met in somatic cancer contexts and do not provide a germline trio result.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• Case records identify NM_001982.4:c.310G>A (ERBB3 p.Val104Met) but contain no proband phenotype, family-history assessment, parental genotypes, or confirmed maternity/paternity results.
• ClinVar and literature records available for this variant describe somatic cancer or functional contexts, not a germline de novo clinical trio observation.

Still missing

• Document the proband's disease phenotype and confirm it matches the disease under evaluation.
• Document family history or absence of family history.
• Obtain confirmed maternity and paternity and parental genotypes demonstrating the variant is absent in both parents.

Reasoning

No qualifying germline case-control comparison was identified for ERBB3 NM_001982.4:c.310G>A (NP_001973.2:p.(Val104Met)). The literature_pass.json criteria index listed PMID:22918138 and PMID:34131312 for PS4; the available abstract for PMID:22918138 is a general AMP report without variant-specific affected/control counts, and PMID:34131312 is a general chromosomal microarray standard that does not mention ERBB3 or this variant. PMID:29533785 mentions ERBB3V104M in a functional-annotation context but provides no affected-patient/control counts. COSMIC reports 132 somatic observations, which is not a germline affected-versus-unaffected case-control comparison. Therefore, no OR or 95% CI can be computed and the ACMG PS4 threshold cannot be evaluated.

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.

Evidence considered

• literature_pass.json criteria_index listed PMID:22918138 and PMID:34131312 for PS4; PMID:22918138 is a general AMP report and PMID:34131312 is a chromosomal microarray technical standard, neither supplying variant-specific affected/control counts.
• PMID:29533785 explicitly mentions ERBB3V104M but supplies no variant-specific affected-case frequency, control frequency, case-control comparison, OR, or 95% CI.
• COSMIC reports 132 somatic observations, but these observations are not a germline case-control comparison.
• gnomAD v4.1 reports 1/1,614,096 alleles overall and 1/1,180,020 European non-Finnish alleles; without affected-case frequency and a matched study design, these data do not provide the required PS4 OR and 95% CI.

Still missing

• A qualifying case-control study or matched-ancestry affected/control counts for NM_001982.4:c.310G>A are needed to calculate OR and its 95% CI.

Sources

Reasoning

The available evidence does not document an affected proband carrying NM_001982.4:c.310G>A with a second pathogenic ERBB3 variant, nor does it provide parental or offspring testing establishing phase. Although biallelic ERBB3 disease is described in the case context, this case contains no qualifying observation that places the evaluated variant in trans with a pathogenic variant. PM3 therefore cannot be assessed from the available evidence.

Rule

PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.

Evidence considered

• The case evidence contains no affected-proband report for NM_001982.4:c.310G>A with a second pathogenic ERBB3 variant.
• The case evidence contains no parental testing, offspring testing, or other validated phase determination for this variant.
• Available ClinVar and cancer-literature records describe somatic or functional observations and do not provide qualifying recessive allelic evidence for PM3.

Still missing

• A documented affected proband with NM_001982.4:c.310G>A and a pathogenic variant in the same gene is needed.
• Parental or offspring testing, or equivalent validated phasing, is needed to establish that the variants are in trans.

Reasoning

The available bundle does not identify a different missense substitution at ERBB3 residue Val104 that has been established as pathogenic. The current variant's own somatic oncogenic classification and the Cancer Hotspots residue observation do not by themselves establish the required different pathogenic missense comparator.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The PM5 candidate artifact reports zero same-residue candidates and explicitly says classic PM5 semantics could not be confirmed.
• ClinVar variation 376410 concerns the observed Val104Met variant itself and does not provide a different pathogenic missense substitution at Val104.
• Ng et al. 2018 discusses ERBB3V104M itself, not a different pathogenic missense change at residue 104.

Still missing

• A validated pathogenic comparator missense variant at ERBB3 residue 104 is needed.

Sources

Reasoning

PM6 cannot be assessed because no clinical de novo observation is documented for this variant. In particular, the available records provide neither an affected proband phenotype nor parental testing showing that the variant is absent in the parents, even without confirmed maternity or paternity.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• Available case records contain no parental genotypes, trio testing result, or clinical de novo report for NM_001982.4:c.310G>A.
• The available variant-specific records concern somatic cancer observations and do not establish a germline de novo event in an affected patient.

Still missing

• Document the proband's disease phenotype.
• Provide parental testing showing the variant is absent in both parents.
• Clarify whether maternity and paternity were confirmed; if not, retain the result as assumed rather than confirmed de novo.

Reasoning

PP1 cannot be assessed because no affected family members, informative meioses, variant-positive relatives, or phenotype-segregation data are documented. Although ERBB3 germline disease context is mentioned elsewhere in the case materials, those records do not provide the multiple affected relatives and segregation observations required for PP1 in this case.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.

Evidence considered

• The case materials contain no pedigree, affected-relative genotypes, unaffected-relative genotypes, informative meioses, or segregation table for NM_001982.4:c.310G>A.
• No publication in the available paper extracts reports family segregation for ERBB3 p.Val104Met.

Still missing

• Identify affected relatives and document their disease phenotypes.
• Provide genotype results for affected and unaffected informative relatives.
• Report the number of informative meioses and whether the variant tracks with disease.

Reasoning

The evidence does not establish both required gene-level components for PP2: a low rate of benign missense variation and missense variants as a common disease mechanism. The available ERBB3 evidence supports a germline loss-of-function disease context and somatic gain-of-function oncology context, but it does not provide a validated benign-missense rate or a disease-specific demonstration that missense variation is the common mechanism for the applicable disorder.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The case identifies a biallelic ERBB3 loss-of-function syndrome context, but that does not establish PP2's required common missense mechanism.
• The case identifies somatic ERBB3 gain-of-function oncology evidence, but somatic oncogenicity does not establish the generic germline PP2 gene-level requirement.

Still missing

• A validated gene-level assessment of benign missense constraint is needed.
• A disease-relevant assessment showing that missense variants are a common ERBB3 disease mechanism is needed.

Reasoning

The case materials do not provide a patient phenotype, family history, suspected disease diagnosis, or phenotype-to-disease match for NM_001982.4:c.310G>A. The available literature concerns somatic cancer or functional annotation and does not establish that this patient's phenotype is highly specific for a single-gene ERBB3 disorder. PP4 therefore cannot be assessed.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The case materials contain no patient phenotype or family-history information relevant to PP4.
• The retrieved literature provides somatic cancer and functional annotation context, not a specific patient phenotype for this case.

Still missing

• Patient phenotype and family-history details, including the suspected disease diagnosis and specificity of its features, are needed.

Reasoning

BS2 is not assessed. The available population data show zero homozygotes in gnomAD v4.1, but absence of homozygotes is not evidence that the variant was observed in a healthy adult. No qualifying healthy-adult carrier observation, disease-specific inheritance model, or documentation that full penetrance is expected at an early age was provided. The available ERBB3 context describes a biallelic multisystem syndrome, but it does not establish the BS2 applicability and penetrance requirements for this missense variant.

Rule

BS2

Evidence considered

• gnomAD v4.1 reports total homozygotes=0 and population homozygotes=0; this is absence of an observation, not a qualifying BS2 observation.
• The case summary identifies a biallelic ERBB3 multisystem syndrome but provides no healthy-adult carrier report or criterion-specific penetrance assessment.

Still missing

• No documented healthy adult carrying the variant in the required zygosity or hemizygosity state
• No disorder-specific evidence that full penetrance is expected at an early age
• Inheritance and penetrance model for this missense variant are not established

Sources

Reasoning

BS4 cannot be assessed because the available records do not identify affected family members who were tested for the variant. There are therefore no documented genotype-negative affected relatives from whom lack of segregation could be concluded, and no information to evaluate phenocopies or multiple pathogenic variants in the family.

Rule

Lack of segregation in affected members of a family. ... Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals.

Evidence considered

• No pedigree or family-testing data document an affected relative who lacks NM_001982.4:c.310G>A.
• The available variant-specific literature and database records do not provide non-segregation evidence in an affected family.

Still missing

• Identify affected relatives and document their clinical phenotypes.
• Provide validated variant testing for affected relatives.
• Assess phenocopies and the possibility of more than one pathogenic variant if an affected relative lacks the variant.

Reasoning

The available evidence does not establish that ERBB3 disease is caused primarily by truncating variants. Although a biallelic ERBB3 loss-of-function syndrome is described, the supplied evidence does not provide the required disease-specific variant spectrum showing that truncating variants primarily account for disease, and the current variant is a missense substitution.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The case summary reports biallelic ERBB3 loss-of-function variants in a multisystem syndrome, but does not establish that truncating variants are the primary known disease mechanism across the relevant disorder.
• The observed variant is a missense substitution, confirmed as NM_001982.4:c.310G>A (p.Val104Met).

Still missing

• A validated disease-specific ERBB3 variant spectrum demonstrating that truncating variants primarily cause disease is needed.

Reasoning

The available evidence does not document a pathogenic variant in the same individual or family that is in trans with NM_001982.4:c.310G>A for a fully penetrant dominant disorder, or in cis with it under any inheritance pattern. No phase, inheritance, or qualifying affected-proband observation is provided, so BP2 cannot be assessed.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• The case evidence contains no documented pathogenic variant paired with NM_001982.4:c.310G>A in cis or in trans.
• The case evidence contains no validated phase or inheritance information for a pathogenic allele at the ERBB3 locus.
• Available ClinVar and cancer-literature records do not establish the allelic configuration required for BP2.

Still missing

• A documented pathogenic variant in the same individual or family is needed.
• Validated phasing is needed to determine whether the variants are in trans or cis.
• For the trans pathway, documentation that the relevant disorder is fully penetrant and dominant is needed.

Reasoning

No qualifying case documents this exact variant in a patient whose disease has an independently established alternate molecular basis. Somatic cancer observations and the report of ERBB3 p.R667S in a different tumor do not establish BP5 for NM_001982.4:c.310G>A/p.Val104Met. BP5 cannot be assessed from the available evidence.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• The case materials contain no alternate molecular diagnosis linked to a patient carrying NM_001982.4:c.310G>A.
• The available report of somatic ERBB3 p.R667S concerns a different variant and does not establish BP5 for p.Val104Met.

Still missing

• A documented patient case with the exact variant and an independently established alternate molecular basis for the phenotype is needed.