Is CDKN2A p.Ser56= (c.168C>T) pathogenic?

CDKN2A p.Ser56= (c.168C>T) is classified Conflicting classifications of pathogenicity in CDKN2A (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-10-01). Very rare (popmax 0.0011%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Ser56= (c.168C>T)?

CDKN2A p.Ser56= (c.168C>T) is associated with hereditary neoplastic syndrome, familial melanoma (ClinVar).

How common is CDKN2A p.Ser56= (c.168C>T) in the general population?

CDKN2A p.Ser56= (c.168C>T) is very rare (popmax 0.0011%, nfe) (gnomAD).

CDKN2A p.Ser56=

c.168C>T · rs771138120 · VCV491567

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0011%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.18	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP 0.25, phastCons 0.014
Overall
CADD	9.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% European (non-Finnish) · 13/1,178,828 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.0009% 13/1,445,236 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDKN2A
Protein: p.Ser56=
Coding: c.168C>T
MANE Select: NM_000077
dbSNP: rs771138120
Type: single nucleotide variant
Location: chr9:21971191 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 56: a UniProt-annotated variant site (in cmm2); the 'interaction with cdk5rap3 and mdm2' region; the 'disordered' region

Full CDKN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial melanoma

Similar variants

CDKN2A p.Ser56Ile Pathogenic/Likely pathogenic ★★ same residue
CDKN2A p.Gly56Arg Uncertain significance ★★ same residue
CDKN2A p.Ser56Arg Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ser56Asn Uncertain significance ★★ ⚠ same residue
CDKN2A p.Gly56= Benign/Likely benign ★★ same residue
CDKN2A p.Ser56Gly Uncertain significance ★ ⚠ same residue
CDKN2A p.Ser56fs Pathogenic ★ same residue
CDKN2A c.150+1G>A Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdkn2a-p-ser56 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown