CALM2 p.Met72Val
c.214A>G · rs2465708894 · VCV2303554
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.757 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.21 | constrained · MANE · 16 kb · p 6.7e-26 · regional, not allelic |
| Overall | ||
| CADD | 28.1 | 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
- CALM2
- Protein
- p.Met72Val
- Coding
- c.214A>G
- MANE Select
- NM_001743
- dbSNP
- rs2465708894
- Type
- single nucleotide variant
- Location
- chr2:47162357 (GRCh38)
- Gene constraint
- LOEUF 0.262 · pLI 0.99 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 21 PDB
- Residue 72
- the ef-hand 2 domain; an α-helix
Similar variants
- CALM2 p.Asn98Ser Pathogenic ★★ same condition
- CALM2 c.-2G>C Uncertain significance ★★ same condition
- CALM2 c.-4C>T Uncertain significance ★★ same condition
- CALM2 p.Arg107Cys Uncertain significance ★★ same condition
- CALM2 p.Glu140= Uncertain significance ★★ same condition
- CALM2 p.Val36Ile Uncertain significance ★★ same condition
- CALM2 p.Asp81= Benign/Likely benign ★★ same condition
- CALM2 p.Glu55= Likely benign ★★ 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/calm2-p-met72val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown