Is CDK13 p.Ala167= (c.501G>A) pathogenic?

CDK13 p.Ala167= (c.501G>A) is classified Likely benign in CDK13 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-19). Very rare (popmax 0.00543%, nfe).

How common is CDK13 p.Ala167= (c.501G>A) in the general population?

CDK13 p.Ala167= (c.501G>A) is very rare (popmax 0.00543%, nfe) (gnomAD).

CDK13 p.Ala167=

c.501G>A · rs999406904 · VCV2413230

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00543%, nfe)

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 1.8	GERP 0.56, phastCons 1
Overall
CADD	13.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00543% European (non-Finnish) · 54/994,888 alleles

Filtering AF 0.00425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.00603% 75/1,242,796 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0446%	2,244
Remaining individualsnot grpmax-eligible	0.0238%	4,205
Finnishnot grpmax-eligible	0.00621%	16,101
European (non-Finnish)grpmax	0.00543%	18,424

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ala167=
Coding: c.501G>A
MANE Select: NM_003718
dbSNP: rs999406904
Type: single nucleotide variant
Location: chr7:39951142 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 167: the 'disordered' region

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

Similar variants

CDK13 p.Ala167Gly Uncertain significance ★★ ⚠ same residue
CDK13 p.Ala167Thr Uncertain significance ★ ⚠ same residue
CDK13 p.Ala167Val 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-ala167 (accessed [today's date]).

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