ABCC2 c.-89G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Dubin-Johnson syndrome
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 -0.27 | GERP -4.9 |
| Non-coding constraint | Z 1.93 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 1.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ABCC2
- Coding
- c.-89G>A
- MANE Select
- NM_000392
- dbSNP
- rs2037637000
- Type
- single nucleotide variant
- Location
- chr10:99782756 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
Disease context
Dubin-Johnson syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Dubin-Johnson syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult
Similar variants
- ABCC2 c.1031+4A>G Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3258+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.333+1G>A Likely pathogenic ★★ same condition
- ABCC2 c.3415-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3741+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.3741+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 c.576+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC2 p.Arg1066Ter Pathogenic/Likely pathogenic ★★ 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/abcc2-c-minus-89g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown