Is CHEK1 p.Pro230= (c.690T>C) pathogenic?

CHEK1 p.Pro230= (c.690T>C) is classified Likely benign in CHEK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-07). No allele count reported in gnomAD v4.1 (AN 1,606,234).

How common is CHEK1 p.Pro230= (c.690T>C) in the general population?

CHEK1 p.Pro230= (c.690T>C) is no allele count reported in gnomAD v4.1 (AN 1,606,234) (gnomAD).

CHEK1 p.Pro230=

c.690T>C · rs2498305394 · VCV1756123

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,606,234)

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 1.9	GERP 1.3, phastCons 1
Overall
CADD	11.35	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,606,234). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHEK1
Protein: p.Pro230=
Coding: c.690T>C
MANE Select: NM_001114122
dbSNP: rs2498305394
Type: single nucleotide variant
Location: chr11:125635505 (GRCh38)
Gene constraint: LOEUF 0.831 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 77.04 · 168 PDB
Residue 230: the protein kinase domain; the 'interaction with clspn' region

Full CHEK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHEK1 p.Gln346Ter Likely pathogenic ★★ same type
CHEK1 p.Arg277Gln Uncertain significance ★★ ⚠ same type
CHEK1 p.Arg420= Benign ★★ same type
CHEK1 p.Ile471Val Benign ★★ same type
CHEK1 c.-160C>T Uncertain significance ★ same type
CHEK1 c.-83T>C Uncertain significance ★ same type
CHEK1 p.Ala200Ser Uncertain significance ★ ⚠ same type
CHEK1 p.Ala34Pro Uncertain significance ★ ⚠ 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/chek1-p-pro230 (accessed [today's date]).

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