Is CDKN2C p.Gly160Arg (c.478G>A) pathogenic?

CDKN2C p.Gly160Arg (c.478G>A) is classified Likely benign in CDKN2C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-12). AlphaMissense: likely benign (0.2532); Very rare (popmax 0.00818%, afr).

How common is CDKN2C p.Gly160Arg (c.478G>A) in the general population?

CDKN2C p.Gly160Arg (c.478G>A) is very rare (popmax 0.00818%, afr) (gnomAD).

What do computational predictors say about CDKN2C p.Gly160Arg (c.478G>A)?

AlphaMissense predicts likely benign (score 0.2532) — an in-silico prediction, not a clinical call.

CDKN2C p.Gly160Arg

c.478G>A · rs956412807 · VCV3141670

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2532 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00818%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2532	likely benign
REVEL	0.161	moderately benign-leaning
SaProt	LLR -7.01	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP -1.2, phastCons 0.99
Regional constraint	o/e 0.76	unconstrained · MANE · 3,898 bp · p 0.00048 · regional, not allelic
Overall
CADD	17.56	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00818% African / African-American · 6/73,350 alleles

Filtering AF 0.00353% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00243%

Overall 0.000893% 14/1,568,202 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00818%	12,225
European (non-Finnish)	0.000692%	144,527

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: CDKN2C
Protein: p.Gly160Arg
Coding: c.478G>A
MANE Select: NM_078626
dbSNP: rs956412807
Type: single nucleotide variant
Location: chr1:50974241 (GRCh38)
Gene constraint: LOEUF 0.94 · pLI 0.21 (gnomAD)
Structure: AlphaFold pLDDT 92.36 · 6 PDB

Full CDKN2C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDKN2C p.Asn159= Likely benign ★★ same type
CDKN2C p.Ala127Asp Uncertain significance ★ ⚠ same type
CDKN2C p.Ala161Gly Uncertain significance ★ ⚠ same type
CDKN2C p.Ala77Val Uncertain significance ★ ⚠ same type
CDKN2C p.Arg39Ser Uncertain significance ★ ⚠ same type
CDKN2C p.Asp17His Uncertain significance ★ ⚠ same type
CDKN2C p.Asp17Tyr Uncertain significance ★ ⚠ same type
CDKN2C p.Asp64His Uncertain significance ★ ⚠ same type

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/cdkn2c-p-gly160arg (accessed [today's date]).

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