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CDKN2A
Final classification
Likely Pathogenic
CDKN2A c.151G>T · p.Val51Phe
CDKN2A

PM1 (moderate): Val51 is located in the second ankyrin repeat domain of p16INK4a, a critical functional domain essential for CDK4/CDK6 binding. Multiple pathogenic missense variants cluster in the ankyrin repeat domains and no benign variation is observed at this residue in population databases.

Gene
CDKN2A
Transcript
NM_000077.4
HGVS · transcript:coding
NM_000077.4:c.151G>T
Consequence
N/A
GRCh38
chr9:21971208 C>A
GRCh37
chr9:21971207 C>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: PS3 supporting, PM1 moderate, PM2 moderate, PP2 supporting; combination = 2 moderate + 2 supporting, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, PM1 moderate, PM2 moderate, PP2 supporting; combination = 2 moderate + 2 supporting, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PP2 Likely Pathogenic
CDKN2A c.151G>T

PM1 (moderate): Val51 is located in the second ankyrin repeat domain of p16INK4a, a critical functional domain essential for CDK4/CDK6 binding. Multiple pathogenic missense variants cluster in the ankyrin repeat domains and no benign variation is observed at this residue in population databases.1 PM2 (moderate): The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, confirming it is not a common population polymorphism.2 PS3 (supporting): A functional study (PMID:10468619) demonstrated that p.Val51Phe fails to inhibit CDK4 kinase activity and is unable to induce G1 arrest in a p16-null cell line, consistent with loss of tumor suppressor function. Verification of full text is pending. PP2 (supporting): CDKN2A is a tumor suppressor gene in which missense variants are a well-established mechanism of disease, with a low rate of benign missense variation in critical functional domains. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two moderate criteria (PM1 + PM2) plus two supporting criteria (PS3 + PP2) meets the threshold for Likely Pathogenic (2 Moderate + 2 Supporting).3 CAUTION: PS3 is derived from a single functional study (PMID:10468619) identified by automated literature search; the full text has not been independently verified. If PS3 is not upheld on human review, the combination would be 2 Moderate + 1 Supporting, which does not meet the Likely Pathogenic threshold and would default to Variant of Uncertain Significance. ClinVar classification is Uncertain significance (2 clinical laboratories, criteria provided, single submitter). This variant has been observed once in somatic cancers (COSMIC COSV105891454).4

PS3 + PM1 + PM2 + PP2 Likely Pathogenic
Gene diagram · NM_000077.4 · variants mapped to exon structure
CDKN2A NM_000077.4
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      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 has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 2735266)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.561. BayesDel score = 0.136755.
      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. CDKN2A, which encodes both a cyclin-dependent kinase inhibitor and an MDM2 inhibitor, is altered by mutation and deletion in various cancers.
      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; COSV105891454, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 9 further PMIDs triaged but not cited — see Sources & References.
      PMID 10468619
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      17047042 ↗ High-risk melanoma susceptibility genes and pancreatic cancer, neural system tumors, and uveal melanoma across GenoMEL. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      31672839 ↗ Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium. CLINVAR
      7987388 ↗ Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR
      40674536 ↗ CDKN2A Cancer Predisposition. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR