Is CDK11B p.Ser386= (c.1158C>T) pathogenic?

CDK11B p.Ser386= (c.1158C>T) is classified Likely benign in CDK11B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). Rare (popmax 0.53%, sas).

How common is CDK11B p.Ser386= (c.1158C>T) in the general population?

CDK11B p.Ser386= (c.1158C>T) is rare (popmax 0.53%, sas) (gnomAD).

CDK11B p.Ser386=

c.1158C>T · rs558767900 · VCV2638051

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.53%, sas)

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 -0.8	GERP -3.6
Overall
CADD	3.583	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.53% South Asian · 483/91,070 alleles

Filtering AF 0.491% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.476%

Overall 0.0352% 568/1,613,694 alleles · rare exomes 535/1,461,390 · genomes 33/152,304 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.53%	189
Remaining individualsnot grpmax-eligible	0.0304%	3,287
Admixed American	0.00667%	15,001
European (non-Finnish)	0.005%	19,994
African / African-American	0.004%	25,020

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: CDK11B
Protein: p.Ser386=
Coding: c.1158C>T
MANE Select: NM_033486
dbSNP: rs558767900
Type: single nucleotide variant
Location: chr1:1640370 (GRCh38)
Gene constraint: LOEUF 0.902 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.24 · 7 PDB
Residue 386: the 'disordered' region

Full CDK11B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDK11B p.Arg109Gly Uncertain significance ★ ⚠ same type
CDK11B p.Arg591Leu Uncertain significance ★ ⚠ same type
CDK11B p.Asp40Gly Uncertain significance ★ same type
CDK11B p.Ala399= Likely benign ★ same type
CDK11B p.Gln384= Likely benign ★ same type
CDK11B p.Ile484= Likely benign ★ same type
CDK11B p.Ile499= Likely benign ★ same type
CDK11B p.Lys551= Likely benign ★ 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/cdk11b-p-ser386 (accessed [today's date]).

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