Is CDK7 p.Leu340Ser (c.1019T>C) pathogenic?

CDK7 p.Leu340Ser (c.1019T>C) is classified Uncertain significance in CDK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-26). AlphaMissense: likely benign (0.206); Absent from gnomAD v4.1.

How common is CDK7 p.Leu340Ser (c.1019T>C) in the general population?

CDK7 p.Leu340Ser (c.1019T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK7 p.Leu340Ser (c.1019T>C)?

AlphaMissense predicts likely benign (score 0.206) — an in-silico prediction, not a clinical call.

CDK7 p.Leu340Ser

c.1019T>C · VCV3489564

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.206 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.206	likely benign
REVEL	0.203	benign-leaning
SaProt	LLR -5.79	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 42 kb · p 2.4e-06 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: CDK7
Protein: p.Leu340Ser
Coding: c.1019T>C
MANE Select: NM_176816 · reported on NM_001799
Type: single nucleotide variant
Location: chr5:69277113 (GRCh38)

Full CDK7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/cdk7-p-leu340ser (accessed [today's date]).

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