CALM1 p.Arg91Gln
c.272G>A · VCV3903346
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.56e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.52 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP -0.24, phastCons 1 |
| Regional constraint | o/e 0.13 | constrained · MANE · 7,483 bp · p 2.4e-32 · regional, not allelic |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.56e-05%
European (non-Finnish) · 1/1,167,970 alleles
Overall
6.9e-05%
1/1,448,468 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
- CALM1
- Protein
- p.Arg91Gln
- Coding
- c.272G>A
- MANE Select
- NM_006888
- Type
- single nucleotide variant
- Location
- chr14:90403955 (GRCh38)
- Gene constraint
- LOEUF 0.276 · pLI 0.99 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.22 · 351 PDB
- Residue 91
- the ef-hand 3 domain; an α-helix; the 'necessary and sufficient for interaction with pcp4' region
Similar variants
- CALM1 p.Arg91= Likely benign ★★ same residue
- CALM1 p.Asn98Ser Pathogenic/Likely pathogenic ★★ same type
- CALM1 p.Asp130Gly Pathogenic/Likely pathogenic ★★ same type
- CALM1 p.Glu140Val Likely pathogenic ★★ same type
- CALM1 c.4-3T>C Uncertain significance ★★ same type
- CALM1 p.Arg87His Uncertain significance ★★ same type
- CALM1 p.Glu120Lys Uncertain significance ★★ same type
- CALM1 p.Tyr100Cys 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/calm1-p-arg91gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown