Is CDK13 p.Ala93Val (c.278C>T) pathogenic?

CDK13 p.Ala93Val (c.278C>T) is classified Conflicting classifications of pathogenicity in CDK13 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-02-22). AlphaMissense: likely benign (0.1426); Very rare (popmax 0.0093%, eas); Associated with Inborn genetic diseases.

What condition is associated with CDK13 p.Ala93Val (c.278C>T)?

CDK13 p.Ala93Val (c.278C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDK13 p.Ala93Val (c.278C>T) in the general population?

CDK13 p.Ala93Val (c.278C>T) is very rare (popmax 0.0093%, eas) (gnomAD).

What do computational predictors say about CDK13 p.Ala93Val (c.278C>T)?

AlphaMissense predicts likely benign (score 0.1426) — an in-silico prediction, not a clinical call.

CDK13 p.Ala93Val

c.278C>T · rs1258245330 · VCV2173037

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1426 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0093%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1426	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -6.60	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 5.3	GERP 0.57, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 47 kb · p 8.4e-05 · regional, not allelic
Overall
CADD	23.5	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 0.0093% East Asian · 3/32,244 alleles

Filtering AF 0.00246% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00128%

Overall 0.000376% 5/1,328,042 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0093%	10,748
Remaining individualsnot grpmax-eligible	0.00199%	50,228
European (non-Finnish)	9.56e-05%	1,046,108

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: CDK13
Protein: p.Ala93Val
Coding: c.278C>T
MANE Select: NM_003718
dbSNP: rs1258245330
Type: single nucleotide variant
Location: chr7:39950919 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 93: the 'disordered' region

Full CDK13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDK13 p.Ala1301Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala134Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala182Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala331Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala504Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala970Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Arg1366Cys Uncertain significance ★★ ⚠ same condition
CDK13 p.Arg197Ser Uncertain significance ★★ ⚠ 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/cdk13-p-ala93val (accessed [today's date]).

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