CANT1 p.Leu384=
c.1152G>C · rs145794847 · VCV792842
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.356%, eas)
Conditions
1
Desbuquois dysplasia 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 -2.1 | GERP -3.2 |
| Overall | ||
| CADD | 0.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.356%
East Asian · 160/44,888 alleles
Filtering AF
0.311%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.294%
Overall
0.0106%
171/1,614,280 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.356% | 281 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.00333% | 30,015 |
| South Asian | 0.0011% | 91,092 |
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.Leu384=
- Coding
- c.1152G>C
- MANE Select
- NM_001159773
- dbSNP
- rs145794847
- Type
- single nucleotide variant
- Location
- chr17:78993604 (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 384
- a β-strand
Similar variants
- CANT1 c.836-9G>A Pathogenic/Likely pathogenic ★★ same condition
- CANT1 p.Arg300Cys Pathogenic/Likely pathogenic ★★ same condition
- CANT1 p.Glu215Lys Pathogenic/Likely pathogenic ★★ same condition
- CANT1 p.Pro245Leu Pathogenic/Likely pathogenic ★★ same condition
- CANT1 p.Pro299Leu Likely pathogenic ★★ same condition
- CANT1 p.Trp247Arg Likely pathogenic ★★ same condition
- CANT1 p.Val226Met Pathogenic ★★ same condition
- CANT1 c.835+6A>G Uncertain significance ★★ same condition
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-leu384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown