CANT1 p.Ser345=
c.1035G>A · rs750928256 · VCV2970526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, 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 -2.5 | GERP -3.2 |
| Overall | ||
| CADD | 8.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00241%
Overall
0.000744%
12/1,613,966 alleles · ultra-rare
exomes 10/1,461,744 · genomes 2/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| Finnishnot grpmax-eligible | 0.00626% | 15,975 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| African / African-American | 0.00133% | 74,934 |
| South Asian | 0.0011% | 91,092 |
| European (non-Finnish) | 0.000254% | 393,349 |
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.Ser345=
- Coding
- c.1035G>A
- MANE Select
- NM_001159773
- dbSNP
- rs750928256
- Type
- single nucleotide variant
- Location
- chr17:78993721 (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 345
- a binding site; a β-strand
Similar variants
- CANT1 p.Ser345Leu 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-ser345 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown