Is CDK12 p.Ala1101= (c.3303A>G) pathogenic?

CDK12 p.Ala1101= (c.3303A>G) is classified Likely benign in CDK12 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-10). Absent from gnomAD v4.1.

How common is CDK12 p.Ala1101= (c.3303A>G) in the general population?

CDK12 p.Ala1101= (c.3303A>G) is absent from gnomAD v4.1 (gnomAD).

CDK12 p.Ala1101=

c.3303A>G · VCV3830482

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 3.9	GERP 0.79, phastCons 1
Overall
CADD	12.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDK12
Protein: p.Ala1101=
Coding: c.3303A>G
MANE Select: NM_016507
Type: single nucleotide variant
Location: chr17:39524881 (GRCh38)
Gene constraint: LOEUF 0.21 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 51.39 · 39 PDB

Full CDK12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDK12 p.Ala1101Glu Uncertain significance ★ ⚠ same residue
CDK12 p.Ala1101Ser Uncertain significance ★ ⚠ same residue
CDK12 p.Ala1101Val Uncertain significance ★ ⚠ same residue
CDK12 c.2108+56T>A Benign/Likely benign ★★ same type
CDK12 c.2666+17A>C Benign ★★ same type
CDK12 c.2769-74G>A Benign ★★ same type
CDK12 c.2846+157G>T Benign ★★ same type
CDK12 c.2963+111T>A 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/cdk12-p-ala1101 (accessed [today's date]).

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