NM_007194.4:c.176C>A

CHEK2 · NP_009125.1:p.(Thr59Lys) · NM_007194.4

GRCh37: chr22:29130534 G>T · GRCh38: chr22:28734546 G>T

Gene: CHEK2 Transcript: NM_007194.4

Final call

VUS

PS3 moderate PM2 supporting

Variant details

Gene

CHEK2

Transcript

NM_007194.4

Protein

NP_009125.1:p.(Thr59Lys)

gnomAD AF

3.841635396580697e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_007194.4:c.176C>A (p.Thr59Lys) is a missense variant in exon 2 of CHEK2, located in the N-terminal SQ/TQ regulatory domain.

This variant has been observed in gnomAD at extremely low frequency: v2.1 AF=0.00159% (4/251,456 alleles) and v4.1 AF=0.00384% (62/1,613,896 alleles), meeting PM2 at supporting strength.

T59K was directly tested in a yeast-based DNA damage response complementation assay and demonstrated intermediate functional impairment (score 0.51, normalized to wild-type=1.00 and kinase-dead control=0.00), consistent with partial loss of CHEK2-mediated DNA damage response. This meets PS3 at moderate strength (single publication, direct variant testing in a heterologous functional system).

CHEK2 T59K was originally reported in four Icelandic breast cancer patients and additional individuals with colon, ovarian, and gastric cancers, although at frequencies not significantly different from controls.

In silico predictions are conflicting and do not provide consensus: REVEL score is borderline (0.513), PolyPhen-2 predicts benign (0.30), BayesDel is below damaging threshold (0.410), and SIFT provides no prediction for this residue. SpliceAI predicts no splicing impact (max delta 0.00).

The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel CHEK2 specification (VCEP v1.0) provides no per-criterion rules; generic ACMG/AMP 2015 criteria were applied.

No additional pathogenic or likely pathogenic criteria were met. The variant is classified as a Variant of Uncertain Significance (VUS) based on one moderate criterion (PS3) and one supporting criterion (PM2).

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	PVS1 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice). NM_007194.4:c.176C>A is a missense variant (p.Thr59Lys) and does not meet generic PVS1 null-variant criteria.
PS1	Not met	No evidence that a different nucleotide change at the same position produces the same amino acid change (p.Thr59Lys) with a known pathogenic classification.
PS2	Not met	No confirmed de novo observation of NM_007194.4:c.176C>A has been reported in the literature or ClinVar submissions.
PS3	Met	CHEK2 T59K was directly tested in a yeast-based DNA damage response complementation assay (Roeb et al. 2012, PMID:22419737) and demonstrated intermediate functional impairment (score 0.51 on a scale normalized to 1.00 wild-type and 0.00 kinase-dead control). The variant was significantly impaired relative to wild-type but retained partial function. Single publication with direct variant testing in a heterologous system qualifies for moderate-strength PS3.	PMID:22419737
PS4	Not met	No statistically significant case-control enrichment has been demonstrated for NM_007194.4:c.176C>A. The variant was reported in 4 Icelandic breast cancer patients and additional cancer-affected individuals (PMID:12052256) but has also been observed in control populations and at low frequency in gnomAD (62 alleles in v4.1), precluding application of PS4.	PMID:12052256
PS5	Not met	No evidence that a different pathogenic variant has been reported at nucleotide position c.176.
PM1	Not met	T59K is located in the N-terminal SQ/TQ domain (residues ~19-69) of CHEK2, an unstructured regulatory region containing ATM/ATR phosphorylation motifs. This region is not a well-established critical functional domain with statistically significant clustering of pathogenic missense variants. The residue is not flagged as a significant hotspot by cancerhotspots.org. Neither the FHA domain nor the kinase domain — the two domains with well-characterized pathogenic missense clustering — are affected.	PMID:22419737
PM2	Met	NM_007194.4:c.176C>A is present in gnomAD at extremely low frequency: v2.1 AF=0.00159% (4/251,456 alleles, 0 homozygotes) and v4.1 AF=0.00384% (62/1,613,896 alleles, 0 homozygotes). The grpmax filtering allele frequency is 1.121e-05 in v2.1 and 4.019e-05 in v4.1. All values are well below the 0.1% PM2 threshold. No homozygotes observed.	gnomad_v2 gnomad_v4
PM5	N/A	No pathogenic missense variant at the same residue (Thr59) was identified. PM5 candidate harvesting returned zero same-residue comparator variants.
PM6	Not met	No confirmed de novo observation of NM_007194.4:c.176C>A has been reported.
PP1	Not met	Familial segregation data reported by Ingvarsson et al. (PMID:12052256) is incomplete and does not support PP1. In one family with colon cancer, a third affected member did not carry T59K. In a second family with breast cancer, two affected individuals did not carry T59K. The absence of complete segregation and co-occurrence of non-carrier affected relatives precludes application of PP1.	PMID:12052256
PP2	Not met	PP2 is applicable to genes where missense variants are a predominant disease mechanism and the gene has a low rate of benign missense variation. CHEK2 has both truncating (e.g., c.1100delC) and missense pathogenic variants. The most prevalent pathogenic variant is a frameshift, and the gene does not meet the PP2 requirement for a gene where missense is the primary mechanism.
PP3	Not met	In silico predictions are conflicting and do not reach consensus. REVEL score is borderline (0.513), BayesDel is below threshold (0.410), PolyPhen-2 predicts benign (0.30), and SIFT provides no prediction for this residue. SpliceAI delta score is 0.00. Roeb et al. (PMID:22419737) reported an in silico consensus of 'no consensus' (nc) across Align-GVGD, PolyPhen-2, and SIFT. The totality of in silico evidence is inconclusive.	revel bayesdel spliceai PMID:22419737
PP4	Not met	No evidence that the patient's phenotype or family history is highly specific for CHEK2-related cancer predisposition relative to other hereditary cancer syndromes. The cancers reported in T59K carriers (breast, colon, ovarian, gastric) overlap with multiple hereditary cancer syndromes and are not uniquely specific to CHEK2.	PMID:12052256
PP5	Not met	ClinVar variation ID 142041 is classified as Uncertain Significance by 12 clinical laboratories with review status 'criteria provided, single submitter.' There is no expert panel (3-star) classification. Under the global PP5 rule requiring ClinVar 3-star expert panel classification, PP5 is not met.	clinvar
BA1	Not met	The maximum allele frequency in gnomAD is 0.00508% (NFE, v4.1), well below the 1% BA1 threshold.	gnomad_v4
BS1	Not met	The maximum allele frequency in gnomAD is 0.00508% (NFE, v4.1), well below the 0.3% BS1 threshold.	gnomad_v4
BS2	Not met	No evidence that T59K has been observed in healthy adults at an age where full penetrance of CHEK2-related cancer predisposition would be expected, with a frequency sufficient to rule out pathogenicity.
BS3	Not met	The only published functional assay for T59K (PMID:22419737) demonstrated intermediate functional impairment (score 0.51), not wild-type-like function. This result does not support a benign classification — it indicates partial loss of function.	PMID:22419737
BS4	Not met	No evidence of lack of segregation with disease in affected families. The two families reported by Ingvarsson et al. (PMID:12052256) showed incomplete segregation, which is not sufficient to demonstrate non-segregation for BS4 application.	PMID:12052256
BP1	Not met	BP1 applies when a missense variant is found in a gene for which only truncating variants are known to cause disease. CHEK2 has well-established pathogenic missense variants (e.g., p.I157T, p.R117G, p.R145W) and the most common pathogenic variant (c.1100delC) is truncating. The gene does not meet the BP1 criterion of being a gene where only truncating variants cause disease.
BP2	Not met	No evidence of NM_007194.4:c.176C>A occurring in trans with a known pathogenic CHEK2 variant has been reported.
BP3	N/A	BP3 is for in-frame deletions/insertions in repetitive regions. This is a missense substitution.
BP4	Not met	While some in silico tools predict a benign effect (PolyPhen-2: 0.30 benign; SpliceAI: 0.00), other predictors are conflicting or borderline (REVEL: 0.513; Align-GVGD: C65 highest risk). The overall in silico evidence does not convincingly support a benign interpretation.	revel bayesdel spliceai PMID:22419737
BP5	Not met	No observation of NM_007194.4:c.176C>A occurring in trans with a known pathogenic CHEK2 variant has been reported.
BP6	Not met	No reputable source classifies NM_007194.4:c.176C>A as benign or likely benign. ClinVar classification is VUS with 1-star review status. Under the global BP6 rule requiring ClinVar 3-star expert panel classification, BP6 is not met.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_007194.4:c.176C>A is a missense variant (p.Thr59Lys).

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