Is CDK13 p.Glu215Asp (c.645G>T) pathogenic?

CDK13 p.Glu215Asp (c.645G>T) is classified Conflicting classifications of pathogenicity in CDK13 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-12-26). AlphaMissense: likely benign (0.1437); Very rare (popmax 0.00796%, amr); Associated with CDK13-related disorder.

What condition is associated with CDK13 p.Glu215Asp (c.645G>T)?

CDK13 p.Glu215Asp (c.645G>T) is associated with CDK13-related disorder (ClinVar).

How common is CDK13 p.Glu215Asp (c.645G>T) in the general population?

CDK13 p.Glu215Asp (c.645G>T) is very rare (popmax 0.00796%, amr) (gnomAD).

What do computational predictors say about CDK13 p.Glu215Asp (c.645G>T)?

AlphaMissense predicts likely benign (score 0.1437) — an in-silico prediction, not a clinical call.

CDK13 p.Glu215Asp

c.645G>T · rs1185235703 · VCV2349856

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1437 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00796%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CDK13-related disorder

Computational evidence

Protein change
AlphaMissense	0.1437	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -6.15	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 4.8	GERP -0.36, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 47 kb · p 8.4e-05 · regional, not allelic
Overall
CADD	19.81	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 0.00796% Admixed American · 2/25,130 alleles

Filtering AF 0.00132% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000492%

Overall 0.000147% 2/1,362,472 alleles · very rare

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.Glu215Asp
Coding: c.645G>T
MANE Select: NM_003718
dbSNP: rs1185235703
Type: single nucleotide variant
Location: chr7:39951286 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 215: the 'disordered' region

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

Disease context

CDK13-related disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDK13 p.Lys734Arg Pathogenic/Likely pathogenic ★★ same condition
CDK13 p.Thr876Ile Likely pathogenic ★★ same condition
CDK13 p.Tyr870Cys Likely pathogenic ★★ same condition
CDK13 p.Asp797His Likely pathogenic ★ same condition
CDK13 p.Gly744Val Likely pathogenic ★ same condition
CDK13 p.Ser864Ter Likely pathogenic ★ same condition
CDK13 p.Tyr891His Likely pathogenic ★ same condition
CDK13 p.Arg890Ter Conflicting classifications of pathogenicity ★ ⚠ 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-glu215asp (accessed [today's date]).

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