ABCC2 p.Tyr52Ter
c.156T>A · rs1554845888 · VCV502331
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 32 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.88 | GERP -5.4, phastCons 0.008 |
| Overall | ||
| CADD | 27.7 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- Protein
- p.Tyr52Ter
- Coding
- c.156T>A
- MANE Select
- NM_000392
- dbSNP
- rs1554845888
- Type
- single nucleotide variant
- Location
- chr10:99784730 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 52
- an α-helix
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-p-tyr52ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown