Is CDK7 p.Arg309Ser (c.927A>T) pathogenic?

CDK7 p.Arg309Ser (c.927A>T) is classified Uncertain significance in CDK7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-27). AlphaMissense: likely pathogenic (0.8176); Absent from gnomAD v4.1.

How common is CDK7 p.Arg309Ser (c.927A>T) in the general population?

CDK7 p.Arg309Ser (c.927A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK7 p.Arg309Ser (c.927A>T)?

AlphaMissense predicts likely pathogenic (score 0.8176) — an in-silico prediction, not a clinical call.

CDK7 p.Arg309Ser

c.927A>T · rs2531576990 · VCV2274005

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8176 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8176	likely pathogenic
REVEL	0.287	benign-leaning
SaProt	LLR -8.97	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 42 kb · p 2.4e-06 · regional, not allelic
Overall
CADD	22.2	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

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.Arg309Ser
Coding: c.927A>T
MANE Select: NM_176816 · reported on NM_001799
dbSNP: rs2531576990
Type: single nucleotide variant
Location: chr5:69276605 (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-arg309ser (accessed [today's date]).

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