GNA11 c.626A>C, p.Gln209Pro

Reasoning

GNA11 p.Gln209Pro lies at codon 209, a statistically significant cancer hotspot reported by Cancer Hotspots. Independent literature shows that GNA11 codon 209 is recurrently mutated in melanocytic tumors, and PMID:29490280 describes codon 209 as an activating hotspot in uveal melanoma. The queried variant is absent from gnomAD v2.1 and v4.1, with no benign population observation supplied for this hotspot. Because no VCEP covers GNA11, the generic hotspot route of PM1 applies.

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 result for GNA11 Q209: the queried variant lies in a statistically significant hotspot.
• PMID:21083380, Results—Sequencing: GNA11 codon 209 was recurrently mutated across melanocytic neoplasms, including the CAG→CCG Q209P substitution.
• PMID:29490280, Introduction: activating GNA11 mutations in uveal melanoma occur at codons Gln209 or Arg183; the study's functional model used GNA11Q209L.
• gnomAD v2.1 and gnomAD v4.1: the queried p.Gln209Pro variant was absent.

Sources

Reasoning

PM2 Supporting is met. NM_002067.5:c.626A>C (GNA11 p.Gln209Pro) was reported absent from gnomAD v2.1 and gnomAD v4.1, and the available non-cancer checks also reported absence in GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER. Thus the variant is absent from the available large population control datasets and is below the generic supporting PM2 threshold of <=0.0001. No FAF calculation is available because the variant was not observed. The generic rule is applied without a VCEP-specific population source because no VCEP covers GNA11.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1: the variant was reported absent.
• gnomAD v4.1: the variant was reported absent.
• GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER also reported the variant absent; the v2 non-cancer source was assessed using its exome-only context and v3 non-cancer using genomes only as specified for those datasets.
• Generic calibration supplied for this case: PM2 Supporting threshold <=0.0001, ClinGen SVI recommendation as supplied with ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

The queried variant is the novel missense substitution GNA11 p.Gln209Pro. A different missense substitution at the same residue, p.Gln209Leu, is documented in PMID:26825879 and was directly studied in PMID:29490280; the latter reports constitutive GNA11 signaling, RasGRP3-dependent growth, and tumorigenic melanocytic lesions in GNA11Q209L models. These variant-specific functional and disease observations establish Q209L as a pathogenic/oncogenic comparator at residue 209 for the generic PM5 same-residue rule. Human review is retained because the evidence is predominantly somatic cancer evidence rather than a germline disease series.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• PMID:26825879, Case Presentation: a somatic GNA11 Q209L mutation was detected at codon 209 in a metastatic melanoma lesion.
• PMID:29490280: GNA11Q209L was tested in conditional mouse and engineered-cell models and produced constitutive Gα11/q-associated signaling, RasGRP3-dependent growth, and melanocytic neoplastic lesions.

Sources

Reasoning

The variant is a missense substitution, NM_002067.5:c.626A>C (p.Gln209Pro), so the applicable generic computational path is REVEL only; SpliceAI is not used for PP3/BP4 in this situation. REVEL is 0.869, meeting the supplied PP3 moderate threshold of >= 0.773 but not the strong threshold of >= 0.932. BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_002067.5:c.626A>C is an exonic missense variant producing p.(Gln209Pro), selecting the REVEL path only.
• Local REVEL lookup reports 0.869 for the queried variant.
• The supplied ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997) sets PP3 moderate at >= 0.773 and PP3 strong at >= 0.932; 0.869 therefore supports PP3 at moderate strength.
• SpliceAI max delta 0.004 is not counted for a missense PP3 assessment, and BayesDel has no established generic ACMG-strength calibration.

Sources

Reasoning

The queried variant is GNA11 p.Gln209Pro (c.626A>C). PMID:21083380 reports the same nucleotide and amino-acid change among somatic GNA11 codon-209 mutations, but the paper does not establish this variant as pathogenic; it reports sequencing observations without variant-specific functional, clinical, segregation, or population evidence. The available ClinVar record is a single-submitter somatic classification and cannot by itself establish PS1. Therefore, a previously established pathogenic occurrence of the same amino-acid change is not demonstrated for this criterion.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• PMID:21083380, Results—Sequencing: GNA11 codon 209 mutations included CAG→CCG (Q209P, corresponding to c.626A>C), but the study supplied no variant-specific pathogenic determination.
• ClinVar variation 4974586: exact p.Gln209Pro record classified Pathogenic by one single submitter with somatic origin; this classification was not used as independent proof of PS1.

Sources

Reasoning

The governing PP5 rule concerns a reputable source reporting the variant as pathogenic when the evidence is unavailable for independent evaluation. The exact-variant ClinVar record is Pathogenic but has review status 'criteria provided, single submitter' and zero expert-panel submissions; it is an ordinary laboratory submission, not an expert-panel classification. The literature reviewed does not provide a qualifying reputable-source pathogenic assertion for this exact variant under the required rule, so PP5 is not met.

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 exact variant NM_002067.5(GNA11):c.626A>C (p.Gln209Pro), variation 4974586: Pathogenic, review status 'criteria provided, single submitter', one clinical laboratory, and expert_panel_submissions = 0; this does not qualify as an expert-panel classification.

Sources

Reasoning

BA1 is not met. NM_002067.5:c.626A>C (GNA11 p.Gln209Pro) was absent from gnomAD v2.1 and gnomAD v4.1, including the available non-cancer subset checks; therefore no filtering allele frequency (grpmax FAF) reaches the generic stand-alone threshold of >=0.05. No population-specific point estimate is available to override the absence finding. The generic BA1 threshold is not reached, and the variant's single-submitter pathogenic ClinVar record is not used as population evidence.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1: NM_002067.5:c.626A>C was reported absent; no allele count, point estimate, or grpmax FAF was available.
• gnomAD v4.1: NM_002067.5:c.626A>C was reported absent; no allele count, point estimate, or grpmax FAF was available.
• The non-cancer checks also reported absence in GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER; no governing VCEP specifies a different population source because no VCEP covers GNA11.
• Generic calibration supplied for this case: BA1 stand-alone threshold >=0.05, ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

BS1 is not met on the available population data. NM_002067.5:c.626A>C was absent from gnomAD v2.1 and gnomAD v4.1, as well as the available non-cancer subset checks, so there is no filtering allele frequency (grpmax FAF) above the generic default of >=0.01. Because the variant is absent, the ancestry, disease-prevalence, penetrance, and allelic-heterogeneity caveat does not create a positive BS1 signal; no maximum-credible-frequency calculation is needed for an elevated frequency that is not observed.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• gnomAD v2.1: the variant was reported absent, so no filtering allele frequency or grpmax FAF was available.
• gnomAD v4.1: the variant was reported absent, so no filtering allele frequency or grpmax FAF was available.
• The non-cancer checks also reported absence in GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER.
• The generic BS1 default supplied for this case is >=0.01; the requested filtering allele-frequency metric is grpmax FAF rather than the popmax point estimate.
• The population-frequency caveat from Whiffin et al. 2017 (PMID:28518168) is not triggered because no elevated ancestry-specific frequency is observed.

Sources

Reasoning

The variant is a missense substitution, so BP4 is assessed through the REVEL path only; the SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.869, which is above the supplied BP4 supporting threshold of <= 0.29 and therefore does not support no impact. The SpliceAI max delta of 0.004 is not counted for missense BP4, and BayesDel is not used because no generic ACMG-strength calibration is established.

Rule

Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_002067.5:c.626A>C is an exonic missense variant, selecting the REVEL path only for BP4.
• Local REVEL lookup reports 0.869 for the queried variant.
• The supplied ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997) sets BP4 supporting at <= 0.29; 0.869 does not meet that threshold.
• SpliceAI max delta 0.004 is not evidence for BP4 in a missense variant, and BayesDel has no established generic ACMG-strength calibration.

Sources

Reasoning

The governing BP6 rule concerns a reputable source reporting the variant as benign when the evidence is unavailable for independent evaluation. The exact-variant ClinVar record is Pathogenic, not benign or likely benign, and has zero expert-panel submissions. No qualifying expert-panel benign classification is present; therefore BP6 is not met.

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 exact variant NM_002067.5(GNA11):c.626A>C (p.Gln209Pro), variation 4974586: Pathogenic, review status 'criteria provided, single submitter', one clinical laboratory, and expert_panel_submissions = 0; no benign expert-panel assertion is available.

Sources

Reasoning

The available case evidence does not provide a proband disease phenotype, family-history assessment, or parental testing establishing both maternity and paternity. Therefore, the required evidence for a confirmed de novo event cannot be assessed.

Rule

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

Evidence considered

• The available case evidence contains no documented proband phenotype, family-history assessment, or parental genotyping results for NM_002067.5:c.626A>C (GNA11 p.Gln209Pro).

Still missing

• Documented proband phenotype and disease diagnosis
• Family-history assessment
• Variant testing of both biological parents confirming maternity and paternity

Reasoning

The exact variant is GNA11 NM_002067.5:c.626A>C, p.(Gln209Pro). PMID:21083380 reports the exact CAG→CCG codon-209 substitution and states that it comprised 2.7% of analyzed GNA11 codon-209 mutations, but it did not perform a variant-specific functional assay for Q209P. PMID:29490280 provides functional evidence for a different same-codon substitution, GNA11Q209L, using engineered melanocytic cells and conditional mouse models, including signaling, growth, and tumorigenesis assays; those results cannot be transferred to Q209P as direct PS3 evidence. PMID:26825879 likewise reports Q209L rather than Q209P and provides no Q209P functional assay. Therefore, the available evidence does not establish a validated, variant-specific in vitro or in vivo functional result for applying PS3.

Rule

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

Evidence considered

• Mutations in GNA11 in uveal melanoma (PMID:21083380), Results/Sequencing: the exact CAG→CCG codon-209 change corresponding to p.Gln209Pro was reported at 2.7% of analyzed codon-209 mutations, but functional assays tested GNA11 Q209L and R183C, not Q209P.
• GNA11 Q209L Mouse Model Reveals RasGRP3 as an Essential Signaling Node in Uveal Melanoma (PMID:29490280): conditional GNA11Q209L mouse and engineered-cell experiments demonstrated signaling, growth, and tumorigenesis effects for Q209L, a different substitution from Q209P.
• GNA11 Mutation in a Patient With Cutaneous Origin Melanoma (PMID:26825879): the reported mutation was Q209L in a single melanoma case, with no functional assay for Q209P.

Still missing

• A validated, variant-specific in vitro or in vivo assay for GNA11 p.Gln209Pro, with appropriate controls and a biologically relevant endpoint, is not available.

Sources

Reasoning

The governing PS4 rule requires a statistically increased prevalence in affected individuals compared with controls, with an RR or OR >5.0 and a confidence interval excluding 1.0. PMID:21083380 reports the exact c.626A>C/p.Q209P change as 2.7% of GNA11 codon-209 mutations among sequenced melanocytic neoplasms, but the extracted report provides no affected-versus-unaffected or population-control counts, no case frequency denominator suitable for comparison, and no RR/OR or confidence interval. The other reviewed papers do not provide case-control evidence for this exact variant. Therefore PS4 cannot be assessed from the available evidence; the 2.7% tumor mutation proportion is not by itself a case-control comparison.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... 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

• PMID:21083380, Results, Sequencing: the exact CAG→CCG codon-209 change corresponding to GNA11 c.626A>C/p.Q209P comprised 2.7% of reported GNA11 codon-209 mutations in the sequenced melanocytic-neoplasm cohort; no control comparison or variant-specific OR/RR was provided in the extracted finding.
• PMID:26825879, Case Presentation/Discussion: reports GNA11 Q209L, not the queried Q209P, in a single metastatic melanoma case and provides no case-control data.
• PMID:29490280, Introduction and functional results: studies GNA11 Q209L rather than Q209P and provides no case-control data for the queried variant.

Still missing

• A case-control dataset for the exact variant with affected and control counts or frequencies is required.
• An RR/OR and 95% confidence interval, or sufficient counts to calculate them, are unavailable.

Sources

Reasoning

PM3 cannot be assessed from the available evidence. The case concerns GNA11 c.626A>C (p.Gln209Pro), but no affected-proband observation, recessive disorder context, second pathogenic allele, parent/offspring testing, or phase result establishes that this variant is in trans with a pathogenic variant. The ClinVar record is a single-submitter somatic classification and does not provide allelic-phase evidence. The reviewed Q209P tumor-sequencing paper reports the variant but provides no segregation or phase data.

Rule

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

Evidence considered

• The case evidence identifies GNA11 c.626A>C (p.Gln209Pro), but contains no affected-proband, second pathogenic allele, parental/offspring testing, or cis/trans phase result.
• ClinVar variation 4974586 is a single-submitter somatic Pathogenic record; it does not document a pathogenic allele in trans or phase testing.
• Van Raamsdonk et al. 2010, PMID:21083380, Results, Sequencing: the paper reports the CAG→CCG codon-209 change corresponding to p.Gln209Pro, but the extracted evidence states that it provides no segregation or phase data.

Still missing

• Establish whether GNA11 p.Gln209Pro is being evaluated in a recessive disorder.
• Obtain an affected-proband observation with a second pathogenic variant in the same gene.
• Obtain parental or offspring testing demonstrating the two variants are in trans.

Sources

Reasoning

The available case evidence does not document a de novo occurrence or parental testing. Without evidence that the variant arose de novo, an assumed-de-novo assessment cannot be made.

Rule

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

Evidence considered

• The available case evidence contains no proband-parent trio results, parental variant findings, or other documentation establishing de novo status for NM_002067.5:c.626A>C (GNA11 p.Gln209Pro).

Still missing

• Evidence that the variant is absent from parental samples or otherwise arose de novo
• Parental testing details, including whether maternity and paternity were confirmed

Reasoning

The available case evidence identifies no affected relatives, family pedigree, segregation testing, or meiosis count. Co-segregation with disease in multiple affected family members therefore cannot be assessed.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• The available case evidence contains no family pedigree, affected-relative clinical information, familial genotyping, or informative meioses for NM_002067.5:c.626A>C (GNA11 p.Gln209Pro).

Still missing

• Pedigree identifying affected relatives
• Genotypes and disease phenotypes of affected family members
• Informative meioses and segregation results

Reasoning

The available evidence does not provide the gene-level facts required by PP2: a low rate of benign missense variation and missense variants as a common mechanism of disease. The reported GNA11 codon-209 cancer hotspot and somatic activating literature do not establish those generic gene-level conditions for the relevant disease context.

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.

Still missing

• A validated gene-level benign-missense constraint assessment and disease-mechanism summary are required.

Reasoning

The governing PP4 rule requires a patient's phenotype or family history highly specific for a disease with a single genetic etiology. The available case materials identify a somatic GNA11 p.Q209P variant and literature tumor contexts, but do not provide a patient phenotype or family history for this case that is highly specific for a single-etiology disease. 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 summary identifies a somatic GNA11 p.Q209P variant but does not document a qualifying patient phenotype or family history for PP4.

Still missing

• A documented patient phenotype or family history and the specific single-etiology disease to which it is highly specific are required.

Reasoning

BS2 was not assessed. The population evidence contains no observation of this variant in a healthy adult, no homozygote or hemizygote observation, and no individual-level phenotype or age information. The available gnomAD records only establish absence, which cannot establish the BS2 healthy-adult observation requirement. A documented healthy adult observation would also require confirmation that the relevant disorder is expected to be fully penetrant at an early age and that the observed zygosity matches the inheritance model.

Rule

Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• gnomAD v2.1 and v4.1 report the variant as absent; they do not provide a healthy-carrier observation or individual-level age and phenotype data.
• The available non-cancer subset checks also report absence and do not supply a qualifying healthy-adult observation.

Still missing

• A verified healthy adult carrying NM_002067.5:c.626A>C, with zygosity, age, phenotype, and relevant inheritance context.
• Confirmation that the relevant disorder has full penetrance expected at an early age for the applicable inheritance model.

Sources

Reasoning

No reviewed source provides a well-established, variant-specific assay showing that GNA11 p.Gln209Pro has no damaging effect on protein function or splicing. PMID:21083380 reports the exact Q209P substitution but does not test its function; PMID:29490280 and PMID:26825879 test or describe Q209L, not Q209P, and therefore cannot establish a benign functional result for this variant. BS3 is consequently not assessed.

Rule

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

Evidence considered

• Mutations in GNA11 in uveal melanoma (PMID:21083380): the exact Q209P substitution was identified by tumor sequencing, but no Q209P assay demonstrated preserved protein function or normal splicing.
• GNA11 Q209L Mouse Model Reveals RasGRP3 as an Essential Signaling Node in Uveal Melanoma (PMID:29490280): functional experiments concerned Q209L rather than Q209P and did not provide benign functional evidence for the queried variant.
• GNA11 Mutation in a Patient With Cutaneous Origin Melanoma (PMID:26825879): the reported alteration was Q209L, not Q209P, and no assay established a neutral effect for Q209P.

Still missing

• A validated, variant-specific functional or splicing assay demonstrating no damaging effect of GNA11 p.Gln209Pro is not available.

Sources

Reasoning

The available case evidence does not identify affected family members or provide their genotypes and phenotypes. Consequently, lack of segregation cannot be evaluated, including the possibility of phenocopies or more than one pathogenic variant 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

• The available case evidence contains no affected-family-member genotypes, phenotypes, pedigree, or non-segregation observations for NM_002067.5:c.626A>C (GNA11 p.Gln209Pro).

Still missing

• Affected family members and their clinical phenotypes
• Variant testing results for affected family members
• Assessment for phenocopies or additional pathogenic variants

Reasoning

The available evidence does not establish that GNA11 is a gene for which primarily truncating variants are known to cause disease. Somatic activating missense observations at codon 209 do not answer the required gene-level truncating-versus-missense disease-mechanism question, and no validated comprehensive variant-spectrum source is available in this evidence set.

Rule

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

Still missing

• A validated gene-level disease variant-spectrum assessment comparing truncating and missense mechanisms is required.

Reasoning

BP2 cannot be assessed from the available evidence. No affected proband or family testing demonstrates GNA11 c.626A>C (p.Gln209Pro) in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant under any inheritance pattern. The available ClinVar entry is a single-submitter somatic classification and the reviewed Q209P tumor-sequencing paper provides no phase or segregation data.

Rule

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 affected-proband observation, parental/offspring testing, or molecular phase result for GNA11 p.Gln209Pro with another pathogenic variant.
• ClinVar variation 4974586 is a single-submitter somatic Pathogenic record; it does not establish cis or trans status with another pathogenic variant.
• Van Raamsdonk et al. 2010, PMID:21083380, Results, Sequencing: the paper reports p.Gln209Pro among tumor mutations but provides no segregation or phase data.

Still missing

• Obtain family or molecular-phasing data for a pathogenic variant in trans or cis.
• Clarify the relevant inheritance pattern and whether a fully penetrant dominant disorder is involved for any trans observation.

Sources

Reasoning

The governing BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. The available exact-variant evidence does not document a qualifying case with an alternate molecular basis for the disease under evaluation. Literature findings about other GNA11 substitutions or unrelated molecular findings cannot be transferred to this variant or case. BP5 therefore cannot be assessed.

Rule

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

Evidence considered

• The reviewed exact-variant evidence reports Q209P in a melanocytic-tumor sequencing cohort but does not document an alternate molecular basis for disease in a qualifying case.

Still missing

• A case report or cohort record for the exact variant documenting an alternate molecular basis for the same disease is required.

Sources