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KEAP1
Final classification
VUS
KEAP1 c.44G>A · p.Arg15Gln
KEAP1

NM_012289.4:c.44G>A (p.Arg15Gln) is a missense variant in exon 2 of KEAP1, a gene in which germline variants cause autosomal dominant familial multinodular goiter.

Gene
KEAP1
Transcript
NM_012289.4
HGVS · transcript:coding
NM_012289.4:c.44G>A
Consequence
N/A
GRCh38
chr19:10499990 C>T
GRCh37
chr19:10610666 C>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: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, 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 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
KEAP1 c.44G>A

NM_012289.4:c.44G>A (p.Arg15Gln) is a missense variant in exon 2 of KEAP1, a gene in which germline variants cause autosomal dominant familial multinodular goiter.1 This variant is present at very low frequency in population databases (gnomAD v2.1: 0.0155%, 40/258,328 alleles; gnomAD v4.1: 0.0196%, 310/1,579,320 alleles) with no homozygotes observed. The overall frequency is below 0.1%, meeting PM2 at a supporting level. Note that the African/African American subpopulation frequency is 0.11%, borderline above the typical 0.1% threshold.2 Multiple lines of computational evidence predict a benign effect: REVEL score 0.053, BayesDel score -0.511, and SpliceAI max delta 0.0, meeting BP4 at a supporting level.3 This variant has been reported once in COSMIC (COSV50285368) in a somatic cancer context and is classified as Uncertain significance in ClinVar by a single clinical laboratory (Ambry Genetics). OncoKB reports unknown oncogenic effect with no variant-specific functional evidence.4 No functional studies, segregation data, de novo reports, or case-control data are available for this variant. The variant does not lie in a mutational hotspot. The overall evidence profile includes one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), consistent with a variant of uncertain significance. Additional evidence such as functional studies, segregation analysis, case-control data, or de novo observations would be needed to refine the classification.

PM2 + BP4 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
Gene diagram · NM_012289.4 · variants mapped to exon structure
KEAP1 NM_012289.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting review Pathogenic
This variant is present at very low frequency in population databases, with an overall allele frequency of 0.0155% (40/258,328 alleles) in gnomAD v2.1 and 0.0196% (310/1,579,320 alleles) in gnomAD v4.1, below the 0.1% threshold. No homozygotes are observed. The highest subpopulation frequency is in the African/African American population at 0.112% (v2.1) and 0.101% (v4.1).
gnomAD v2.1: AF = 0.0155% (40/258328)0 homozygotes
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.053 (well below 0.5), BayesDel score is -0.511 (below 0), and SpliceAI predicts no splicing alteration (max delta = 0.0). All in silico tools agree on a benign prediction.
REVEL: 0.053 (benign)BayesDel (no AF): -0.510705 (benign)SpliceAI: max delta = 0.0 (no predicted splice impact)
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at position c.44 resulting in the same p.Arg15Gln amino acid substitution has been established as pathogenic.
PS2 No de novo occurrence with confirmed paternity and maternity has been reported for this variant.
PS3 No well-established in vitro or in vivo functional studies demonstrating a damaging effect have been identified for NM_012289.4:c.44G>A (p.Arg15Gln).
PS4 No case-control studies demonstrating statistically significant enrichment of this variant in affected individuals compared to controls are available.
PM1 This variant does not lie within a statistically significant mutational hotspot in KEAP1.
PM5 No pathogenic missense variant at the same amino acid residue (Arg15) has been identified.
PM6 No de novo occurrence (without confirmed paternity and maternity) has been reported for this variant.
PP1 No cosegregation data in affected family members is available for this variant.
PP2 KEAP1 missense constraint metrics (e.g., gnomAD missense Z-score, o/e ratio) are not available in the evidence packet.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No patient phenotype or family history data were provided to assess whether the clinical presentation is highly specific for KEAP1-related disease.
PP5 No evidence that this variant was found in a patient with an established alternate genetic cause for disease.
Benign
BA1 The overall allele frequency in gnomAD v2.1 is 0.0155%, far below the BA1 threshold of 1% (and well below 5% even in any subpopulation).
BS1 The overall allele frequency in gnomAD v2.1 is 0.0155%, below the BS1 threshold of 0.3%.
BS2 No data are available documenting observation of this variant in healthy adult individuals for a disorder with full penetrance expected at an early age.
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect have been identified for this variant.
BS4 No segregation data are available to evaluate lack of cosegregation with disease in affected family members.
BP1 KEAP1 germline disease (familial multinodular goiter) is associated with both missense and truncating variants (PMID:39373520 reports p.L136P, p.R415C, p.R483H missense variants alongside p.Q86* and p.V411fs truncating variants).
BP2 No evidence that this variant has been observed in trans with a pathogenic variant in KEAP1 or any other fully penetrant dominant gene.
BP5 No evidence that this variant was found in a case with an alternative molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0.000196287; MAF= 0.01963%, 310/1579320 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.00100647; MAF= 0.10065%, 75/74518 alleles, homozygotes = 0); grpmax FAF= 0.00082258.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000154842; MAF= 0.01548%, 40/258328 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.00111977; MAF= 0.11198%, 27/24112 alleles, homozygotes = 0); grpmax FAF= 0.00070213.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.02% · 310 / 1,579,320
0 hom · FAF 0.082%
African/African American
75 / 74,518
0.1%
European (non-Finnish)
214 / 1,157,622
0.018%
Admixed American
10 / 57,656
0.017%
Remaining individuals
6 / 60,898
0.0099%
South Asian
5 / 87,572
0.0057%
+ 5 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.015% · 40 / 258,328
0 hom · FAF 0.07%
African/African American
27 / 24,112
0.11%
Admixed American
5 / 32,816
0.015%
South Asian
2 / 26,408
0.0076%
European (non-Finnish)
5 / 116,892
0.0043%
European (Finnish)
1 / 23,812
0.0042%
+ 3 not observed (Ashkenazi Jewish, East Asian, Remaining individuals)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 2345816)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.053. BayesDel score = -0.510705.
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. KEAP1, a tumor suppressor and adaptor protein, is recurrently mutated in lung cancer.
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 previously been reported in somatic cancers (COSMIC; COSV50285368, n = 1 times).
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