NM_012289.4:c.1222C>A

KEAP1 · NP_036421.2:p.(Pro408Thr) · NM_012289.4

GRCh37: chr19:10602356 G>T · GRCh38: chr19:10491680 G>T

Gene: KEAP1 Transcript: NM_012289.4

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

KEAP1

Transcript

NM_012289.4

Protein

NP_036421.2:p.(Pro408Thr)

gnomAD AF

1.0772789201863059e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_012289.4:c.1222C>A (p.Pro408Thr) in KEAP1 is a rare missense variant present at extremely low frequency in population databases (gnomAD v2.1 AF=0.00337%, v4.1 AF=0.00108%), satisfying PM2 at supporting strength.

Multiple independent in silico tools (REVEL 0.295, BayesDel -0.344, SpliceAI 0.01) consistently predict no deleterious impact on protein function or splicing, satisfying BP4 at supporting strength.

The variant is classified as Uncertain significance by a single clinical laboratory in ClinVar (VCV2209515). No expert panel review is available, and no variant-specific publications or functional studies were identified.

KEAP1 germline mutations cause familial multinodular goiter, with both truncating and missense variants reported as pathogenic (PMID:39373520). Codon 408 falls within the Kelch repeat domain but is not a statistically significant cancer hotspot residue.

Under the generic ACMG/AMP 2015 classification framework (PMID:25741868), the tally is PM2 (supporting pathogenic) + BP4 (supporting benign). With one supporting criterion for each direction, the combined evidence is insufficient to classify as either likely benign or likely pathogenic, resulting in a final classification of Uncertain significance.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_012289.4:c.1222C>A is a missense variant (p.Pro408Thr) and does not fall into the null-variant categories (nonsense, frameshift, canonical ±1,2 splice) required for PVS1 under the ClinGen SVI PVS1 framework (PMC6185798).	pvs1_generic_framework
PS1	Not met	No alternative nucleotide change at codon 408 resulting in the same Pro408Thr amino acid substitution has been reported as pathogenic. No evidence exists to satisfy PS1.
PS2	Not met	No de novo observation has been reported for this variant. The single ClinVar submission (Ambry Genetics, SCV003527689) did not include parental testing data.	clinvar
PS3	Not met	No variant-specific functional studies have been identified for NM_012289.4:c.1222C>A (p.Pro408Thr). OncoKB classifies this variant as Unknown Oncogenic Effect with no curated functional evidence. The COSMIC entry (COSV105847274, n=1) represents a somatic observation count only, not experimental functional data. The codon 408 position falls within the Kelch repeat domain but has not been included in any systematic functional characterization range (e.g., saturation mutagenesis or tiling screen) spanning this residue.	oncokb
PS4	Not met	No case-control enrichment data are available. The variant is present in gnomAD at very low frequency (v2.1 AF=0.00337%; v4.1 AF=0.00108%) and has a single ClinVar VUS submission. No statistically significant enrichment in affected individuals has been demonstrated.	gnomad_v2 gnomad_v4 clinvar
PS5	N/A	PS5 is not a criterion defined in the ACMG/AMP 2015 sequence variant interpretation guidelines (PMID:25741868) used under the generic_acmg framework. No evidence was assessed under this code.
PM1	Not met	While codon 408 resides within the Kelch repeat domain of KEAP1 (a well-characterized NRF2-binding domain critical for KEAP1 function), cancerhotspots.org does not identify this residue as a statistically significant hotspot (residue_significant: false). The variant is present in gnomAD (7 alleles v2.1, 17 alleles v4.1), indicating some benign variation exists within this domain. Without a residue-specific hotspot designation and with observed population variation, PM1 is not met under the generic ACMG framework.	gnomad_v2 gnomad_v4
PM2	Met	This variant is present in gnomAD at extremely low frequency in population databases: v2.1 AF=3.37e-05 (0.00337%, 7/207,868 alleles, 0 homozygotes) and v4.1 AF=1.08e-05 (0.00108%, 17/1,578,050 alleles, 0 homozygotes). The global allele frequency is well below the 0.1% threshold for PM2 under non-VCEP gnomAD rules. No homozygous individuals have been observed.	gnomad_v2 gnomad_v4
PM5	Not met	No different amino acid change at codon 408 has been identified as pathogenic. The automated PM5 candidate search found no qualifying same-residue comparator variants in ClinVar.	pm5_candidates
PM6	Not met	No de novo observation (confirmed or assumed) has been reported for this variant. PM6 requires at least an assumed de novo event without confirmation of paternity and maternity, which is absent.
PP1	Not met	No co-segregation data are available. No family studies involving this variant have been reported.
PP2	Not met	PP2 requires a low rate of benign missense variation in the gene (e.g., high missense Z-score) and missense variants as a common disease mechanism. While KEAP1 germline missense mutations are a known disease mechanism for familial multinodular goiter (PMID:39373520), population constraint metrics (gnomAD missense Z-score or OE ratio) were not available in the evidence packet to confirm a low rate of benign missense variation.
PP3	Not met	In silico computational tools do not support a deleterious effect: REVEL score 0.295 (below 0.5 threshold, predicts benign), BayesDel score -0.344 (negative, predicts benign), SpliceAI max delta 0.01 (no predicted splice impact). All three independent computational lines agree that this variant is likely benign, which instead supports BP4.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data are available to evaluate whether the clinical presentation is highly specific for a KEAP1-related disorder with a single genetic etiology.
PP5	Not met	ClinVar reports this variant as Uncertain significance (1 submitter, criteria provided, single submitter; not an expert panel). The PP5/BP6 rule requires a 3-star expert panel classification for automatic assignment. The single Ambry Genetics submission (SCV003527689) is classified as VUS with no expert panel designation, and does not meet the threshold for PP5 at any strength level.	clinvar
BA1	Not met	The global population allele frequency in gnomAD v2.1 is 0.00337% (AF=3.37e-05) and in v4.1 is 0.00108% (AF=1.08e-05), both far below the BA1 threshold of 1% (>0.01).	gnomad_v2 gnomad_v4
BS1	Not met	The global population allele frequency in gnomAD v2.1 is 0.00337% and in v4.1 is 0.00108%, both well below the BS1 threshold of 0.3% under non-VCEP gnomAD rules.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age. While the variant is present in gnomAD (7–17 heterozygous carriers among presumably healthy population controls), KEAP1 germline disease (familial multinodular goiter) is adult-onset, variably penetrant, and thyroid-specific. Without evidence of early-age full penetrance and given the low allele count, BS2 cannot be reliably applied. No homozygous individuals have been observed.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrating no deleterious effect have been identified for this variant. In silico predictions alone (BP4) do not constitute functional evidence for BS3.
BS4	Not met	No family segregation data are available. BS4 requires lack of segregation with disease in affected family members, which cannot be evaluated for this case.
BP1	Not met	BP1 applies to missense variants in genes where primarily truncating variants cause disease. KEAP1 germline disease (familial multinodular goiter) is caused by both truncating (p.Q86*, p.V411fs) and missense (p.L136P, p.R415C, p.R483H) variants, as demonstrated in PMID:39373520. Missense variants are an established pathogenic mechanism in KEAP1, so BP1 does not apply.
BP2	Not met	No data are available regarding observation of this variant in trans with a pathogenic variant or in cis with a pathogenic variant. BP2 cannot be evaluated.
BP4	Met	Multiple independent lines of computational evidence consistently predict no deleterious impact: REVEL score 0.295 (below the 0.5 pathogenicity threshold, predicting benign), BayesDel score -0.344 (negative score, predicting benign), and SpliceAI maximum delta 0.01 (no predicted splice-altering effect). This concordance across three in silico tools satisfies BP4 at supporting strength.	revel bayesdel spliceai
BP5	N/A	BP5 is not a criterion defined in the ACMG/AMP 2015 sequence variant interpretation guidelines (PMID:25741868) used under the generic_acmg framework. No evidence was assessed under this code.
BP6	Not met	ClinVar reports this variant as Uncertain significance, not benign. The PP5/BP6 rule requires a 3-star expert panel classification; the single submitter (Ambry Genetics) classification is VUS with no expert panel designation. BP6 is not met.	clinvar
BP7	N/A	NM_012289.4:c.1222C>A is a missense variant (p.Pro408Thr), not a synonymous/silent variant. BP7 applies exclusively to synonymous variants with no predicted splice impact.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.