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GNA11
Final classification
Pathogenic
GNA11 c.626A>T · p.Gln209Leu
GNA11

GNA11 c.626A>T (p.Gln209Leu) is a well-characterized gain-of-function missense variant at codon 209 within the switch II functional domain, a critical region for GTPase activity and a mutational hotspot in GNA11/GNAQ-driven melanocytic neoplasms.

Gene
GNA11
Transcript
NM_002067.5
HGVS · transcript:coding
NM_002067.5:c.626A>T
Consequence
N/A
GRCh38
chr19:3118944 A>T
GRCh37
chr19:3118942 A>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 moderate, PM2 supporting, PP2 supporting, PP3 supporting, PP5 supporting; combination = 1 strong + 1 moderate + 4 supporting, which maps to Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 moderate, PM2 supporting, PP2 supporting, PP3 supporting, PP5 supporting; combination = 1 strong + 1 moderate + 4 supporting, which maps to Pathogenic.
Classification rationale
PS3PS4PM2PP2PP3PP5 Pathogenic
GNA11 c.626A>T

GNA11 c.626A>T (p.Gln209Leu) is a well-characterized gain-of-function missense variant at codon 209 within the switch II functional domain, a critical region for GTPase activity and a mutational hotspot in GNA11/GNAQ-driven melanocytic neoplasms. Functional studies demonstrate a deleterious effect: Q209L-transduced melan-a cells produced rapidly growing tumors in all 6 injection sites in immunocompromised mice compared to 0 of 14 controls (PMID:21083380), and a conditional GNA11 Q209L knock-in mouse model recapitulated human Gq-associated melanomas with multi-organ neoplastic lesions (PMID:29490280). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada across all populations, yet is recurrently observed in affected tissue: COSMIC reports 442 somatic occurrences, and it has been identified as the predominant codon 209 mutation in uveal melanoma, blue nevi, cutaneous melanoma, and phakomatosis pigmentovascularis.1 Two clinical laboratories in ClinVar classify this variant as Pathogenic or Likely Pathogenic (variation ID 376002). In silico prediction with REVEL (score 0.833) supports a damaging effect. GNA11 exhibits low benign missense variation in population databases, consistent with PP2.2 Applying generic ACMG/AMP 2015 combination rules: PS3 (strong), PM1 (moderate), PS4 (moderate), PM2 (supporting), PP2 (supporting), PP3 (supporting), PP5 (supporting) support a classification of Pathogenic.3

PS3 + PS4 + PM2 + PP2 + PP3 + PP5 Pathogenic
2 clinvar ↗revel
3 generic_acmg_combination_rules
Gene diagram · NM_002067.5 · variants mapped to exon structure
GNA11 NM_002067.5
Fetching transcript structure from UCSC…
Applied criteria · 6 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 376002)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.833. BayesDel score = 0.245583.
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV50017277, n = 442 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      21083380 ↗ Mutations in GNA11 in uveal melanoma. ONCOKB
      26825879 ↗ GNA11 Mutation in a Patient With Cutaneous Origin Melanoma: A Case Report. ONCOKB
      29490280 ↗ GNA11 Q209L Mouse Model Reveals RasGRP3 as an Essential Signaling Node in Uveal Melanoma. ONCOKB
      23640210 ↗ The emerging mutational landscape of G proteins and G-protein-coupled receptors in cancer. CLINVAR
      24141786 ↗ Combined PKC and MEK inhibition in uveal melanoma with GNAQ and GNA11 mutations. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26778290 ↗ Mosaic Activating Mutations in GNA11 and GNAQ Are Associated with Phakomatosis Pigmentovascularis and Extensive Dermal Melanocytosis. CLINVAR
      23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR