CALM2 p.Arg91Leu
c.272G>T · rs2103825224 · VCV3061097
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,601,084)
Conditions
1
CALM2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.791 | moderately pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.21 | constrained · MANE · 16 kb · p 6.7e-26 · regional, not allelic |
| Overall | ||
| CADD | 29.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,601,084). 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
- CALM2
- Protein
- p.Arg91Leu
- Coding
- c.272G>T
- MANE Select
- NM_001743
- dbSNP
- rs2103825224
- Type
- single nucleotide variant
- Location
- chr2:47162299 (GRCh38)
- Gene constraint
- LOEUF 0.262 · pLI 0.99 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 21 PDB
- Residue 91
- the ef-hand 3 domain; an α-helix; the 'necessary and sufficient for interaction with pcp4' region
Disease context
CALM2-related disorder
Similar variants
- CALM2 p.Arg91Cys Uncertain significance ★★ same residue
- CALM2 p.Gly133Asp Likely pathogenic ★ same condition
- CALM2 p.Glu46Lys Uncertain significance ★ same condition
- CALM2 c.4-1666C>T Likely benign same condition
- CALM2 p.Asn98Ser Pathogenic ★★ same type
- CALM2 p.Asp134Asn Likely pathogenic ★★ same type
- CALM2 p.Asp96Tyr Pathogenic/Likely pathogenic ★★ same type
- CALM2 p.Asp96Val Pathogenic ★★ 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/calm2-p-arg91leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown