CALM2 p.Thr27=
c.81T>C · VCV3484419
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
1
Cardiovascular phenotype
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 4.1 | GERP -0.19, phastCons 1 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,178,812 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.00131%
2/152,204 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
- CALM2
- Protein
- p.Thr27=
- Coding
- c.81T>C
- MANE Select
- NM_001743
- Type
- single nucleotide variant
- Location
- chr2:47162616 (GRCh38)
- Gene constraint
- LOEUF 0.262 · pLI 0.99 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 21 PDB
- Residue 27
- a binding site; the ef-hand 1 domain; a β-strand
Similar variants
- CALM2 p.Thr27Ser Uncertain significance ★ same residue
- 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
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-thr27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown