Is CDK13 p.Asp797His (c.2389G>C) pathogenic?

CDK13 p.Asp797His (c.2389G>C) is classified Likely pathogenic in CDK13 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-31). AlphaMissense: likely pathogenic (0.9999); Absent from gnomAD v4.1; Associated with CDK13-related disorder.

What condition is associated with CDK13 p.Asp797His (c.2389G>C)?

CDK13 p.Asp797His (c.2389G>C) is associated with CDK13-related disorder (ClinVar).

How common is CDK13 p.Asp797His (c.2389G>C) in the general population?

CDK13 p.Asp797His (c.2389G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK13 p.Asp797His (c.2389G>C)?

AlphaMissense predicts likely pathogenic (score 0.9999) — an in-silico prediction, not a clinical call.

CDK13 p.Asp797His

c.2389G>C · VCV4895789

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9999 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

CDK13-related disorder

Computational evidence

Protein change
AlphaMissense	0.9999	likely pathogenic ✓ concordant with ClinVar · top 4% in CDK13
REVEL	0.641	indeterminate
SaProt	LLR -15.39	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.36	constrained · MANE · 81 kb · p 2.9e-34 · regional, not allelic
Overall
CADD	33.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDK13
Protein: p.Asp797His
Coding: c.2389G>C
MANE Select: NM_003718
Type: single nucleotide variant
Location: chr7:40045871 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 797: the protein kinase domain; a β-strand

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.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
CDK13 p.Asn842Ile 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-asp797his (accessed [today's date]).

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