CANT1 p.Arg63=
c.189C>T · rs2071079259 · VCV2758442
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 0.32 | GERP -0.78, phastCons 0.86 |
| Overall | ||
| CADD | 4.875 | 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
- CANT1
- Protein
- p.Arg63=
- Coding
- c.189C>T
- MANE Select
- NM_001159773
- dbSNP
- rs2071079259
- Type
- single nucleotide variant
- Location
- chr17:78997434 (GRCh38)
- Gene constraint
- LOEUF 1.239 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.47 · 4 PDB
Similar variants
- CANT1 p.Arg63His Uncertain significance ★★ ⚠ same residue
- CANT1 p.Arg63Ser Uncertain significance ★★ ⚠ same residue
- CANT1 p.Arg63Cys Uncertain significance ★ ⚠ same residue
- CANT1 p.Arg63fs Pathogenic/Likely pathogenic ★★ same residue
- CANT1 c.836-9G>A Pathogenic/Likely pathogenic ★★ same type
- CANT1 p.Arg300Cys Pathogenic/Likely pathogenic ★★ same type
- CANT1 p.Glu215Lys Pathogenic/Likely pathogenic ★★ same type
- CANT1 p.Glu215Ter 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/cant1-p-arg63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown