CANT1 p.Ser168=
c.504C>T · rs751857487 · VCV1573731
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0129%, nfe)
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 -20 | GERP -3.2 |
| Overall | ||
| CADD | 0.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0129%
European (non-Finnish) · 152/1,180,050 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00985%
159/1,614,058 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0129% | 7,763 |
| Admixed American | 0.00333% | 29,994 |
| South Asian | 0.00329% | 30,363 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
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.Ser168=
- Coding
- c.504C>T
- MANE Select
- NM_001159773
- dbSNP
- rs751857487
- Type
- single nucleotide variant
- Location
- chr17:78997119 (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 168
- a binding site; a β-strand
Similar variants
- CANT1 p.Ser168Cys Uncertain significance ★ ⚠ 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
- CANT1 p.Pro245Leu Pathogenic/Likely pathogenic ★★ same type
- CANT1 p.Pro299Leu Likely pathogenic ★★ same type
- CANT1 p.Trp247Arg 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-ser168 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown