CANT1 p.Ser256=
c.768C>T · rs777545339 · VCV1528743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 0.42 | GERP -2.9, phastCons 0.98 |
| Overall | ||
| CADD | 11.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,052 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00447%
72/1,610,366 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,052 |
| East Asian | 0.0112% | 8,962 |
| European (non-Finnish) | 0.00526% | 19,009 |
| Admixed American | 0.00336% | 29,777 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,168 |
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
- CANT1
- Protein
- p.Ser256=
- Coding
- c.768C>T
- MANE Select
- NM_001159773
- dbSNP
- rs777545339
- Type
- single nucleotide variant
- Location
- chr17:78995085 (GRCh38)
- Gene constraint
- LOEUF 1.239 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.47 · 4 PDB
- Residue 256
- a functional site (important for dimer formation)
Similar variants
- 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
- CANT1 p.Pro245Leu Pathogenic/Likely pathogenic ★★ same type
- CANT1 p.Pro299Leu Likely pathogenic ★★ same type
- CANT1 p.Trp247Arg Likely pathogenic ★★ same type
- CANT1 p.Trp86Ter Pathogenic/Likely 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-ser256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown