Is CDK13 p.Thr670Arg (c.2009C>G) pathogenic?

CDK13 p.Thr670Arg (c.2009C>G) is classified Benign in CDK13 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.189); Rare (popmax 0.546%, nfe).

How common is CDK13 p.Thr670Arg (c.2009C>G) in the general population?

CDK13 p.Thr670Arg (c.2009C>G) is rare (popmax 0.546%, nfe) (gnomAD).

What do computational predictors say about CDK13 p.Thr670Arg (c.2009C>G)?

AlphaMissense predicts likely benign (score 0.189) — an in-silico prediction, not a clinical call.

CDK13 p.Thr670Arg

c.2009C>G · rs34775357 · VCV717025

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.189 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.546%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.189	likely benign
REVEL	0.145	moderately benign-leaning
SaProt	LLR -7.02	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 1.5, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 47 kb · p 8.4e-05 · regional, not allelic
Overall
CADD	22.4	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 0.546% European (non-Finnish) · 6,438/1,179,796 alleles

Filtering AF 0.534% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.53%

Overall 0.447% 7,208/1,613,690 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.546%	183
Finnishnot grpmax-eligible	0.483%	207
Remaining individualsnot grpmax-eligible	0.392%	255
Admixed American	0.135%	740
Ashkenazi Jewishnot grpmax-eligible	0.132%	759
South Asian	0.0703%	1,422
Middle Eastern	0.066%	1,515
African / African-American	0.0373%	2,679

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.Thr670Arg
Coding: c.2009C>G
MANE Select: NM_003718
dbSNP: rs34775357
Type: single nucleotide variant
Location: chr7:39997631 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 670: the 'disordered' region; a UniProt-annotated variant site (in)

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

Similar variants

CDK13 p.Thr670Ile Uncertain significance ★ ⚠ same residue
CDK13 p.Thr670Lys Uncertain significance ★ ⚠ same residue
CDK13 p.Thr670Pro Uncertain significance ★ ⚠ same residue
CDK13 p.Ala732Thr Likely pathogenic ★★ same type
CDK13 p.Arg1025Ter Pathogenic/Likely pathogenic ★★ same type
CDK13 p.Arg737Cys Pathogenic ★★ same type
CDK13 p.Arg751Gln Pathogenic/Likely pathogenic ★★ same type
CDK13 p.Arg860Gln Pathogenic/Likely pathogenic ★★ 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-thr670arg (accessed [today's date]).

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