CNNM2 p.Leu321del
c.955CTG[2] · rs1845545201 · VCV996043
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
hypomagnesemia, seizures, and intellectual disability 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.9, phastCons 1 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. 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
- CNNM2
- Protein
- p.Leu321del
- Coding
- c.955CTG[2]
- MANE Select
- NM_017649
- dbSNP
- rs1845545201
- Type
- Microsatellite
- Location
- chr10:102919435 (GRCh38)
- Gene constraint
- LOEUF 0.312 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.70 · 7 PDB
- Residue 321
- the cnnm transmembrane domain
Similar variants
- CNNM2 p.Ala19fs Likely pathogenic ★ same condition
- CNNM2 p.Ile435del Likely pathogenic ★ same condition
- CNNM2 p.Leu739del Uncertain significance ★ same condition
- CNNM2 p.Arg602Ter Likely pathogenic ★★ same condition
- CNNM2 p.Glu122Lys Pathogenic/Likely pathogenic ★★ same condition
- CNNM2 p.Glu357Lys Pathogenic ★★ same condition
- CNNM2 p.Ser269Trp Pathogenic/Likely pathogenic ★★ same condition
- CNNM2 c.1904-6C>G Uncertain significance ★★ same condition
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/cnnm2-p-leu321del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown