Is CDK13 p.Gly256= (c.768C>T) pathogenic?

CDK13 p.Gly256= (c.768C>T) is classified Likely benign in CDK13 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-05-26). Very rare (popmax 0.00334%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CDK13 p.Gly256= (c.768C>T)?

CDK13 p.Gly256= (c.768C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDK13 p.Gly256= (c.768C>T) in the general population?

CDK13 p.Gly256= (c.768C>T) is very rare (popmax 0.00334%, nfe) (gnomAD).

CDK13 p.Gly256=

c.768C>T · VCV3672786

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00334%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.14	GERP 0.87, phastCons 0.96
Overall
CADD	9.973	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00334% European (non-Finnish) · 38/1,138,890 alleles

Filtering AF 0.00248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00217%

Overall 0.00256% 39/1,525,270 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00334%	29,971
Remaining individualsnot grpmax-eligible	0.00169%	59,116

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.Gly256=
Coding: c.768C>T
MANE Select: NM_003718
Type: single nucleotide variant
Location: chr7:39951409 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 256: 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.Gly256Asp Uncertain significance ★ ⚠ same residue
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

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-gly256 (accessed [today's date]).

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