CALM3 p.Asn112=
c.336C>T · rs887745567 · VCV748876
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 4.9 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 14.11 | 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
- CALM3
- Protein
- p.Asn112=
- Coding
- c.336C>T
- MANE Select
- NM_005184
- dbSNP
- rs887745567
- Type
- single nucleotide variant
- Location
- chr19:46608896 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI 0.93 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.45 · 26 PDB
- Residue 112
- the ef-hand 3 domain; an α-helix; the 'necessary and sufficient for interaction with pcp4' region
Similar variants
- CALM3 p.Asn112Lys Uncertain significance ★ ⚠ same residue
- CALM3 p.Asp94Ala Pathogenic/Likely pathogenic ★★ same type
- CALM3 p.Asp96His Pathogenic/Likely pathogenic ★★ same type
- CALM3 p.Glu141Lys Pathogenic ★★ same type
- CALM3 c.34+3G>A Uncertain significance ★★ same type
- CALM3 c.421+5G>A Uncertain significance ★★ same type
- CALM3 p.Ala103Thr Uncertain significance ★★ ⚠ same type
- CALM3 p.Ala148Thr 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/calm3-p-asn112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown