CNNM4 p.Gln717=
c.2151G>A · rs2079236742 · VCV1993967
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.318 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 9.188 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,026 alleles
Overall
6.84e-05%
1/1,461,850 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CNNM4
- Protein
- p.Gln717=
- Coding
- c.2151G>A
- MANE Select
- NM_020184
- dbSNP
- rs2079236742
- Type
- single nucleotide variant
- Location
- chr2:96809340 (GRCh38)
- Gene constraint
- LOEUF 0.794 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.20 · 6 PDB
Similar variants
- CNNM4 p.Gln717Ter Pathogenic/Likely pathogenic ★★ same residue
- CNNM4 p.Arg519Ter Pathogenic ★★ same type
- CNNM4 p.Arg605Ter Pathogenic ★★ same type
- CNNM4 p.Gln564Ter Pathogenic ★★ same type
- CNNM4 c.2130+5G>A Uncertain significance ★★ same type
- CNNM4 c.*1126G>A Uncertain significance ★★ same type
- CNNM4 p.Ala297Gly Uncertain significance ★★ ⚠ same type
- CNNM4 p.Ala35Thr 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/cnnm4-p-gln717 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown