Is CDKN2A p.Ala41Thr (c.121G>A) pathogenic?

CDKN2A p.Ala41Thr (c.121G>A) is classified Uncertain significance in CDKN2A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-26). Very rare (popmax 0.0022%, sas); Associated with familial melanoma.

What condition is associated with CDKN2A p.Ala41Thr (c.121G>A)?

CDKN2A p.Ala41Thr (c.121G>A) is associated with familial melanoma, hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Ala41Thr (c.121G>A) in the general population?

CDKN2A p.Ala41Thr (c.121G>A) is very rare (popmax 0.0022%, sas) (gnomAD).

How is Familial melanoma inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

CDKN2A p.Ala41Thr

c.121G>A · rs1064793582 · VCV419008

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

familial melanoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.315	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 0.52, phastCons 0.96
Overall
CADD	19.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,012 alleles

Filtering AF 0.000689% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000539%

Overall 0.000996% 16/1,605,770 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,506
European (non-Finnish)	0.00119%	84,264

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.Ala41Thr
Coding: c.121G>A
MANE Select: NM_000077 · reported on NM_058195
dbSNP: rs1064793582
Type: single nucleotide variant
Location: chr9:21994211 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 41: an α-helix; the 'interaction with cdk5rap3 and mdm2' region

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

Disease context

familial melanoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Familial melanoma (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial
Onset: Adult
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

CDKN2A p.Pro41Ala Uncertain significance ★★ ⚠ same residue
CDKN2A p.Pro41Arg Uncertain significance ★★ ⚠ same residue
CDKN2A p.Pro41Ser Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala41= Likely benign ★★ same residue
CDKN2A p.Pro41= Benign/Likely benign ★★ same residue
CDKN2A p.Pro41Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Pro41Leu Uncertain significance ★ ⚠ same residue
CDKN2A p.Pro41fs Pathogenic ★★ same residue

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-ala41thr (accessed [today's date]).

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