CABIN1 p.Ser394=
c.1182T>G · rs1601823350 · VCV735391
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.455%, 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 -0.72 | GERP -3, phastCons 0.021 |
| Overall | ||
| CADD | 8.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.455%
European (non-Finnish) · 5,280/1,159,942 alleles
Filtering AF
0.445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.441%
Overall
0.365%
5,807/1,591,524 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.455% | 220 |
| Remaining individualsnot grpmax-eligible | 0.294% | 341 |
| Ashkenazi Jewishnot grpmax-eligible | 0.16% | 626 |
| African / African-American | 0.141% | 711 |
| South Asian | 0.133% | 749 |
| Middle Eastern | 0.133% | 751 |
| East Asian | 0.0852% | 1,173 |
| Finnishnot grpmax-eligible | 0.0282% | 3,544 |
| Admixed American | 0.015% | 6,660 |
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
- CABIN1
- Protein
- p.Ser394=
- Coding
- c.1182T>G
- MANE Select
- NM_012295
- dbSNP
- rs1601823350
- Type
- single nucleotide variant
- Location
- chr22:24056280 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.03 · 1 PDB
- Residue 394
- the 'disordered' region
Similar variants
- CABIN1 p.Arg51Trp Uncertain significance ★★ ⚠ same type
- CABIN1 p.Glu256Lys Uncertain significance ★★ ⚠ same type
- CABIN1 p.Pro1981Leu Uncertain significance ★★ ⚠ same type
- CABIN1 p.Ser222Leu Uncertain significance ★★ ⚠ same type
- CABIN1 c.1262+10A>G Benign/Likely benign ★★ same type
- CABIN1 c.1262+62= Benign ★★ same type
- CABIN1 c.2748+37= Benign ★★ same type
- CABIN1 c.2911-29= Benign ★★ 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/cabin1-p-ser394 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown