Is CDKN2A p.Thr93= (c.279G>T) pathogenic?

CDKN2A p.Thr93= (c.279G>T) is classified Conflicting classifications of pathogenicity in CDKN2A (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-09-25). No allele count reported in gnomAD v4.1 (AN 1,605,514); Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Thr93= (c.279G>T)?

CDKN2A p.Thr93= (c.279G>T) is associated with hereditary neoplastic syndrome, familial melanoma (ClinVar).

How common is CDKN2A p.Thr93= (c.279G>T) in the general population?

CDKN2A p.Thr93= (c.279G>T) is no allele count reported in gnomAD v4.1 (AN 1,605,514) (gnomAD).

CDKN2A p.Thr93=

c.279G>T · rs2131094486 · VCV1059245

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,605,514)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.119	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.77	GERP -0.11, phastCons 0.001
Overall
CADD	8.281	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,605,514). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDKN2A
Protein: p.Thr93=
Coding: c.279G>T
MANE Select: NM_000077
dbSNP: rs2131094486
Type: single nucleotide variant
Location: chr9:21971080 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 93: an α-helix; a UniProt-annotated variant site (in non-small cell lung carcinoma); 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.Thr93Ala Uncertain significance ★★ ⚠ same residue
CDKN2A p.Thr93Arg Uncertain significance ★★ ⚠ same residue
CDKN2A p.Thr93Lys Uncertain significance ★★ ⚠ same residue
CDKN2A p.Thr93Met Uncertain significance ★★ same residue
CDKN2A p.Thr93Pro Uncertain significance ★ ⚠ same residue
CDKN2A p.Thr93Ser Uncertain significance ★ same residue
CDKN2A c.150+1G>A Likely pathogenic ★★ same condition
CDKN2A c.150+2T>G 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-thr93 (accessed [today's date]).

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