Is CCNK p.Ile151Val (c.451A>G) pathogenic?

CCNK p.Ile151Val (c.451A>G) is classified Uncertain significance in CCNK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-20). AlphaMissense: likely pathogenic (0.6917); Very rare (popmax 0.00118%, sas).

How common is CCNK p.Ile151Val (c.451A>G) in the general population?

CCNK p.Ile151Val (c.451A>G) is very rare (popmax 0.00118%, sas) (gnomAD).

What do computational predictors say about CCNK p.Ile151Val (c.451A>G)?

AlphaMissense predicts likely pathogenic (score 0.6917) — an in-silico prediction, not a clinical call.

CCNK p.Ile151Val

c.451A>G · rs1470435323 · VCV2429046

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6917 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00118%, sas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.6917	likely pathogenic
REVEL	0.28	benign-leaning
SaProt	LLR -7.61	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.45	unconstrained · MANE · 1,995 bp · p 1.1e-11 · regional, not allelic
Overall
CADD	26.0	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 0.00118% South Asian · 1/84,834 alleles

Filtering AF 0.000298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000215%

Overall 0.000574% 9/1,567,738 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00118%	84,834
European (non-Finnish)	0.000693%	144,320

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: CCNK
Protein: p.Ile151Val
Coding: c.451A>G
MANE Select: NM_001144995 · reported on NM_001099402
dbSNP: rs1470435323
Type: single nucleotide variant
Location: chr14:99500805 (GRCh38)

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

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/ccnk-p-ile151val (accessed [today's date]).

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