NM_001195132.1:c.226del

CDKN2A · NP_001182061.1:p.(Ala76ProfsTer70) · NM_001195132.1

GRCh37: chr9:21971131 GC>G · GRCh38: chr9:21971132 GC>G

Gene: CDKN2A Transcript: NM_001195132.1

Final call

Likely Pathogenic

PVS1 strong PM1 moderate PM2 moderate

Variant details

Gene

CDKN2A

Transcript

NM_001195132.1

Protein

NP_001182061.1:p.(Ala76ProfsTer70)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_001195132.1:c.226del (p.Ala76ProfsTer70) is a frameshift variant in CDKN2A that introduces a premature termination codon at position 145, removing ankyrin repeats II–IV and the CDK4/CDK6 binding domain. CDKN2A loss of function is an established mechanism in familial melanoma.

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0% across all population databases, well below the PM2 threshold of 0.1%.

The truncated protein loses the CDK4/CDK6 binding domain and ankyrin repeats II–IV. Two independent functional studies demonstrate this region is critical for p16INK4a tumor suppressor activity: the core region 73–131 is necessary for CDK4 inhibition, and premature termination mutants in this region abolish CDK4/CDK6 binding.

No variant-specific functional studies, segregation data, de novo observations, or clinical case reports were identified for this exact variant in the reviewed literature.

Under generic ACMG/AMP 2015 combination rules: PVS1 (strong) + PM1 (moderate) + PM2 (moderate) = Likely Pathogenic (1 strong + 2 moderate).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

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	Met	Frameshift variant NM_001195132.1:c.226del (p.Ala76ProfsTer70) in CDKN2A exon 2 of 4 introduces a premature termination codon at position 145. CDKN2A loss of function is an established mechanism in familial melanoma. The PTC lies approximately 24 bp upstream of the exon 2–3 junction (c.457), raising possibility of NMD escape; under PMC6185798 this warrants PVS1 at strong rather than very strong. The truncated protein loses ankyrin repeats II–IV and the CDK4/CDK6 binding domain.	pvs1_generic_framework
PS1	N/A	This is a single-nucleotide deletion, not a nucleotide substitution at the same position. No known pathogenic SNV exists at c.226 for comparison.
PS2	Not met	No de novo observation with confirmed paternity and maternity has been reported for this variant in any reviewed source.
PS3	Not met	No variant-specific functional data exist for c.226del. PMID:8603820 tested large deletion constructs (9-72, 9-131, 73-131, 73-156) and PMID:8668202 tested eight truncation mutants, but neither study directly assayed p.Ala76ProfsTer70. Domain-level inference from sparse testing does not satisfy PS3 under the governing calibration; this evidence is assigned to PM1.	PMID:8603820 PMID:8668202
PS4	Not met	No case-control association data or statistically significant enrichment in affected individuals has been reported for this variant. PMID:22703879 screened 572 individuals but the abstract does not confirm observation of c.226del; the ClinVar record citing this PMID corresponds to a different variant (NM_000077.5:c.150+76del, intronic).
PS5	Not met	No reputable source (expert panel, clinical diagnostic laboratory) has classified this variant as pathogenic. The sole ClinVar submission (SCV000043253, Biesecker Lab) is a non-exact match for a different variant and reports Uncertain Significance with no assertion criteria.
PM1	Met	The frameshift at codon 76 removes amino acids 76–168, deleting ankyrin repeats II–IV and the CDK4/CDK6 binding domain. Two independent publications demonstrate this region is critical for p16INK4a function: PMID:8603820 shows the core region 73–131 is necessary for CDK4 inhibition; PMID:8668202 shows truncation mutants in this region (e.g., R80ter) abolish CDK4/CDK6 binding and kinase inhibition.	PMID:8603820 PMID:8668202
PM2	Met	This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0 (HostSeq genomes). Allele frequency is below the 0.1% PM2 threshold in all population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM4	N/A	This is a frameshift variant, not an in-frame deletion/insertion or stop-loss variant. PM4 applies only to non-frameshift protein length changes.
PM5	N/A	This is a frameshift variant, not a missense change at a codon where a different missense is known to be pathogenic. PM5 candidate harvesting confirmed no same-residue missense comparators.
PM6	Not met	No de novo observation (with or without confirmed paternity/maternity) has been reported for this variant in any reviewed source.
PP1	Not met	No co-segregation data with disease in families has been reported for this variant.
PP2	N/A	This is a frameshift variant. PP2 applies specifically to missense variants in genes with a low rate of benign missense variation.
PP3	Not met	SpliceAI delta score is 0.00, indicating no predicted splice impact. REVEL and BayesDel scores are unavailable (not an SNV). No in silico evidence supports a pathogenic effect; however, the variant's pathogenicity is through protein truncation, not splicing, so computational splice predictions are not informative for this variant class.	spliceai
PP4	Not met	No patient-specific phenotype data or clinical information has been provided to assess whether the clinical presentation is consistent with CDKN2A-related disease.
PP5	Not met	No reputable source (expert panel, clinical diagnostic laboratory) has classified this variant as pathogenic. ClinVar contains no exact match for this variant. The OncoKB classification of 'Likely Oncogenic' is a somatic cancer annotation and does not constitute germline PP5 evidence.
BA1	Not met	This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, well below the 1% BA1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	This variant is absent from all population databases. Allele frequency of 0% is below the 0.3% BS1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No observation in healthy adult controls has been reported for this variant.
BS3	Not met	No functional studies demonstrating a benign effect for this variant exist. The functional studies reviewed (PMID:8603820, PMID:8668202) demonstrate loss of function for truncating mutations in this region, consistent with a damaging effect, not a benign one.	PMID:8603820 PMID:8668202
BS4	Not met	No non-segregation data in families has been reported for this variant.
BP1	N/A	This is a frameshift variant. BP1 applies specifically to missense variants in genes where the primary disease mechanism is truncating.
BP2	Not met	No observation in trans with a known pathogenic variant has been reported for this variant.
BP3	N/A	This is a frameshift variant, not an in-frame deletion in a repetitive region. BP3 applies to in-frame deletions/insertions in repetitive or non-conserved regions.
BP4	Not met	No multiple lines of benign computational evidence exist. SpliceAI delta is 0.00 (no splice impact), but this is a protein-truncating frameshift variant; the absence of a predicted splice effect does not constitute independent benign evidence for a variant whose pathogenicity is mediated through protein truncation. REVEL/BayesDel are not applicable to indels.	spliceai
BP5	Not met	No alternative molecular basis for disease has been identified to suggest this variant is incidental.
BP6	Not met	No reputable source has classified this variant as benign or likely benign.
BP7	N/A	This is a frameshift deletion, not a synonymous variant with no predicted splice impact. BP7 applies to synonymous and intronic variants.

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