Is CMPK1 p.Ile207Val (c.619A>G) pathogenic?

CMPK1 p.Ile207Val (c.619A>G) is classified Uncertain significance in CMPK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-07). Absent from gnomAD v4.1.

How common is CMPK1 p.Ile207Val (c.619A>G) in the general population?

CMPK1 p.Ile207Val (c.619A>G) is absent from gnomAD v4.1 (gnomAD).

CMPK1 p.Ile207Val

c.619A>G · VCV4004027

Uncertain significance Single submitter

Classification

Uncertain significance

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.
REVEL	0.121	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.1	GERP 2.3, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 43 kb · p 4.9e-10 · regional, not allelic
Overall
CADD	18.74	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: CMPK1
Protein: p.Ile207Val
Coding: c.619A>G
MANE Select: NM_016308
Type: single nucleotide variant
Location: chr1:47375267 (GRCh38)
Gene constraint: LOEUF 0.902 · pLI 0.18 (gnomAD)
Structure: AlphaFold pLDDT 97.06 · 2 PDB

Full CMPK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CMPK1 p.Arg54Leu Uncertain significance ★ same type
CMPK1 p.Arg6Leu Uncertain significance ★ same type
CMPK1 p.Asn156Ser Uncertain significance ★ same type
CMPK1 p.Glu178Lys Uncertain significance ★ same type
CMPK1 p.Gly43Cys Uncertain significance ★ same type
CMPK1 p.Leu10Phe Uncertain significance ★ same type
CMPK1 p.Pro24Thr Uncertain significance ★ same type
CMPK1 p.Ser147Pro 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/cmpk1-p-ile207val (accessed [today's date]).

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