CANT1 p.Ser392=
c.1176C>T · rs147501831 · VCV1643182
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0866%, afr)
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 -6.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.605 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0866%
African / African-American · 65/75,066 alleles
Filtering AF
0.0697%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0635%
Overall
0.00483%
78/1,614,222 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0866% | 1,155 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| Admixed American | 0.00333% | 30,016 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 8.47e-05% | 1,180,045 |
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.Ser392=
- Coding
- c.1176C>T
- MANE Select
- NM_001159773
- dbSNP
- rs147501831
- Type
- single nucleotide variant
- Location
- chr17:78993580 (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 392
- a β-strand
Similar variants
- CANT1 p.Ser392Asn 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-ser392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown