Is CDKN2A c.150+5del pathogenic?

CDKN2A c.150+5del is classified Conflicting classifications of pathogenicity in CDKN2A (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-07-25). Absent from gnomAD; Associated with melanoma and neural system tumor syndrome.

What condition is associated with CDKN2A c.150+5del?

CDKN2A c.150+5del is associated with melanoma and neural system tumor syndrome, hereditary neoplastic syndrome, familial melanoma (ClinVar).

How common is CDKN2A c.150+5del in the general population?

CDKN2A c.150+5del is absent from gnomAD (gnomAD).

How is Melanoma and neural system tumor syndrome inherited?

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

CDKN2A c.150+5del

rs1235245881 · VCV819378

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

melanoma and neural system tumor syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +5	donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.58	GERP -4
Non-coding constraint	Z 5.22	1 kb window · o/e 0.70 · regional · uncalibrated

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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
Coding: c.150+5del
MANE Select: NM_000077
dbSNP: rs1235245881
Type: Deletion
Location: chr9:21974673 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB

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

Disease context

melanoma and neural system tumor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome familial melanoma

For Melanoma and neural system tumor syndrome (Orphanet):

Inheritance: Autosomal dominant, Unknown
Onset: Adult, Elderly

Similar variants

CDKN2A c.193+1del Likely pathogenic ★★ same condition
CDKN2A c.457+1_457+10del Pathogenic/Likely pathogenic ★★ same condition
CDKN2A p.Ala36fs Pathogenic ★★ same condition
CDKN2A p.Ala76fs Pathogenic/Likely pathogenic ★★ same condition
CDKN2A p.Asn71fs Pathogenic/Likely pathogenic ★★ same condition
CDKN2A p.Glu120fs Pathogenic ★★ same condition
CDKN2A p.His123fs Pathogenic ★★ same condition
CDKN2A p.Leu32_Leu37del 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-c-150-plus-5del (accessed [today's date]).

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