Is CDK13 p.1504RG[2] (c.4509CAGAGG[2]) pathogenic?

CDK13 p.1504RG[2] (c.4509CAGAGG[2]) is classified Likely benign in CDK13 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Ultra-rare (popmax 0.0394%, eas).

How common is CDK13 p.1504RG[2] (c.4509CAGAGG[2]) in the general population?

CDK13 p.1504RG[2] (c.4509CAGAGG[2]) is ultra-rare (popmax 0.0394%, eas) (gnomAD).

CDK13 p.1504RG[2]

c.4509CAGAGG[2] · rs747124942 · VCV2890938

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0394%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.53	GERP -0.4, phastCons 1
Overall
CADD	17.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0394% East Asian · 16/40,600 alleles

Filtering AF 0.0247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0201%

Overall 0.00279% 40/1,434,210 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0394%	2,537
Admixed American	0.0131%	7,622
South Asian	0.00368%	27,201
European (non-Finnish)	0.00147%	68,237
African / African-American	0.00144%	69,510

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.1504RG[2]
Coding: c.4509CAGAGG[2]
MANE Select: NM_003718
dbSNP: rs747124942
Type: Microsatellite
Location: chr7:40094948 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB

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

Similar variants

CDK13 p.Ile708del Likely pathogenic ★★ same type
CDK13 p.Leu1418del Uncertain significance ★★ same type
CDK13 c.3029+33_3029+45del Likely benign ★★ same type
CDK13 p.Ala76_Ser77insAla Benign/Likely benign ★★ same type
CDK13 p.Thr1143fs Likely pathogenic ★ same type
CDK13 p.235HS[1] Uncertain significance ★ same type
CDK13 p.Gly256_Arg257insGly Uncertain significance ★ same type
CDK13 p.Gly380_Asp381insGly 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/cdk13-p-1504rg-2 (accessed [today's date]).

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