ATP8B1 p.Ile1237=
c.3711C>T · rs1599060649 · VCV2978743
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000169%, 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 0.58 | GERP 0.61, phastCons 0.1 |
| Overall | ||
| CADD | 6.399 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,002 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,611,542 alleles · very rare
exomes 2/1,459,164 · genomes 0/152,378 · joint denominator
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
- ATP8B1
- Protein
- p.Ile1237=
- Coding
- c.3711C>T
- MANE Select
- NM_001374385
- dbSNP
- rs1599060649
- Type
- single nucleotide variant
- Location
- chr18:57648533 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.42 · 13 PDB
Similar variants
- ATP8B1 c.1473+1G>C Pathogenic ★★ same type
- ATP8B1 c.1819+1G>A Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.2097+2T>C Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.2286-2A>G Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.2418+5G>A Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.3400+2T>C Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.3531+1G>A Pathogenic/Likely pathogenic ★★ same type
- ATP8B1 c.555-1G>C 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/atp8b1-p-ile1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown