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ERBB3
Final classification
VUS
ERBB3 c.244G>A · p.Glu82Lys
ERBB3

NM_001982.3:c.244G>A (p.Glu82Lys) is a missense variant in ERBB3 exon 3.

Gene
ERBB3
Transcript
NM_001982.3
HGVS · transcript:coding
NM_001982.3:c.244G>A
Consequence
N/A
GRCh38
chr12:56085004 G>A
GRCh37
chr12:56478788 G>A
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: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
ERBB3 c.244G>A

NM_001982.3:c.244G>A (p.Glu82Lys) is a missense variant in ERBB3 exon 3. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (0 alleles across all populations), meeting PM2 at moderate strength.1 Multiple in silico predictors support a deleterious effect: REVEL score 0.948 (strongly pathogenic) and BayesDel score 0.443 (intermediate, leaning deleterious), meeting PP3 at supporting strength.2 PVS1 is not applicable as c.244G>A is a missense variant, not a null variant (nonsense, frameshift, or canonical ±1,2 splice). Per ClinGen SVI PVS1 recommendations (PMC6185798), the generic PVS1 framework applies only to predicted null variants.3 The variant is absent from ClinVar, absent from COSMIC, and not located in a statistically significant mutational hotspot (CancerHotspots). No literature PMIDs were identified for this variant. OncoKB classifies it as 'Unknown Oncogenic Effect' without variant-specific functional evidence.4 No de novo, segregation, case-control, functional, or phenotype-specific data are available for this variant; PS2, PS3, PS4, PP1, PP4, PM6, and benign criteria BS2-BS4, BP5-BP6 remain not assessed. PM5 is not applicable as no pathogenic missense comparator at ERBB3 residue E82 was identified. BP7 is not applicable to missense variants.5 Overall classification: 1 moderate pathogenic criterion (PM2) and 1 supporting pathogenic criterion (PP3) are met. Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), this does not reach the Likely Pathogenic threshold (minimum: 3 moderate, or 2 moderate + 2 supporting, or 1 moderate + 4 supporting). The variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + PP3 VUS
2 revelbayesdel
3 pvs1_generic_framework ↗pvs1_variant_assessment
5 pm5_candidates
6 generic_acmg_combination_rules
Gene diagram · NM_001982.3 · variants mapped to exon structure
ERBB3 NM_001982.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_001982.3:c.244G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada. Complete absence from large population databases (allele frequency 0%, well below the 0.1% threshold for PM2) constitutes moderate evidence of pathogenicity under the ACMG/AMP 2015 framework.
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)and gnomAD-Canada (0 alleles).
PP3 supporting Pathogenic
Multiple in silico predictors support a deleterious effect. REVEL score of 0.948 (strongly pathogenic) and BayesDel score of 0.443 (intermediate, leaning deleterious). SpliceAI predicts no splice impact (max delta 0.00), which is expected for an exonic missense. The convergence of REVEL and BayesDel toward a damaging prediction meets PP3 at supporting strength.
REVEL: 0.948 (strongly deleterious)BayesDel: 0.443 (intermediateleaning deleterious)
Assessed · not applied
Pathogenic
PS1 PS1 requires a different nucleotide change resulting in the same amino acid substitution (E82K) previously established as pathogenic.
PS2 PS2 requires a confirmed de novo occurrence with parental confirmation.
PS3 PS3 requires well-established functional studies demonstrating a deleterious effect.
PS4 PS4 requires a statistically significant enrichment in affected individuals versus controls.
PM1 PM1 requires the variant to be located in a mutational hotspot or well-established critical functional domain without benign variation.
PM6 PM6 requires a confirmed de novo occurrence without parental confirmation, or a de novo assumption.
PP1 PP1 requires co-segregation of the variant with disease in multiple affected family members.
PP2 PP2 requires the gene to have a low rate of benign missense variation and for missense variants to be a common disease mechanism.
PP4 PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.
PP5 PP5 requires a reputable source (e.g., expert panel, clinical laboratory) to have recently classified this variant as pathogenic.
Benign
BA1 BA1 requires allele frequency > 1% in population databases.
BS1 BS1 requires allele frequency greater than expected for the disorder (> 0.3% by non-VCEP criteria).
BS2 BS2 requires observation of the variant in a healthy adult for a fully penetrant dominant disorder, or observation in trans with a pathogenic variant for a recessive disorder.
BS3 BS3 requires well-established functional studies demonstrating no deleterious effect.
BS4 BS4 requires lack of segregation of the variant with disease in affected family members.
BP1 BP1 requires a missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 BP2 requires observation of the variant in trans with a pathogenic variant in a fully penetrant recessive disorder, or in cis with a pathogenic variant.
BP4 BP4 requires multiple lines of computational evidence to suggest no impact on gene product.
BP5 BP5 requires the variant to be found in a case with an alternative molecular basis for disease.
BP6 BP6 requires a reputable source to have recently classified this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.948. BayesDel score = 0.443228.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ERBB3, a receptor tyrosine kinase, is altered by mutation or amplification in various cancer types.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots