Is CDK14 p.Ser120Asn (c.359G>A) pathogenic?

CDK14 p.Ser120Asn (c.359G>A) is classified Uncertain significance in CDK14 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-28). AlphaMissense: ambiguous (0.5453); Ultra-rare (popmax 0.0591%, nfe).

How common is CDK14 p.Ser120Asn (c.359G>A) in the general population?

CDK14 p.Ser120Asn (c.359G>A) is ultra-rare (popmax 0.0591%, nfe) (gnomAD).

What do computational predictors say about CDK14 p.Ser120Asn (c.359G>A)?

AlphaMissense predicts ambiguous (score 0.5453) — an in-silico prediction, not a clinical call.

CDK14 p.Ser120Asn

c.359G>A · rs138436598 · VCV2224421

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5453 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0591%, nfe)

Computational evidence

Protein change
AlphaMissense	0.5453	ambiguous
REVEL	0.37	indeterminate
SaProt	LLR -7.38	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 5.6, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 522 kb · p 0.00055 · regional, not allelic
Overall
CADD	26.8	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 0.0591% European (non-Finnish) · 697/1,179,728 alleles

Filtering AF 0.0554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.054%

Overall 0.0457% 737/1,613,350 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0591%	1,693
Remaining individualsnot grpmax-eligible	0.0336%	2,975
African / African-American	0.02%	4,992
Finnishnot grpmax-eligible	0.0047%	21,267
Admixed American	0.00167%	59,934

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: CDK14
Protein: p.Ser120Asn
Coding: c.359G>A
MANE Select: NM_001287135
dbSNP: rs138436598
Type: single nucleotide variant
Location: chr7:90726802 (GRCh38)
Gene constraint: LOEUF 0.894 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.10
Residue 120: the 'disordered' region

Full CDK14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDK14 p.Pro61= Benign ★★ same type
CDK14 c.124-16986G>A Uncertain significance ★ same type
CDK14 c.124-17003A>G Uncertain significance ★ same type
CDK14 c.124-17015A>T Uncertain significance ★ same type
CDK14 p.Ala382Val Uncertain significance ★ ⚠ same type
CDK14 p.Arg117Trp Uncertain significance ★ ⚠ same type
CDK14 p.Arg250His Uncertain significance ★ ⚠ same type
CDK14 p.Arg370Cys 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/cdk14-p-ser120asn (accessed [today's date]).

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