ABCC2 p.Ile1320fs
c.3958del · rs2493048339 · VCV2715705
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 28 of 32 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 1.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- ABCC2
- Protein
- p.Ile1320fs
- Coding
- c.3958del
- MANE Select
- NM_000392
- dbSNP
- rs2493048339
- Type
- Deletion
- Location
- chr10:99844436 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 1320
- a β-strand; the abc transporter 2 domain
Similar variants
- ABCC2 p.Asn159fs Pathogenic ★★ same type
- ABCC2 p.Asn718fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Ile754fs Pathogenic ★★ same type
- ABCC2 p.Leu431fs Pathogenic ★★ same type
- ABCC2 p.Leu788fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Leu809fs Pathogenic/Likely pathogenic ★★ same type
- ABCC2 p.Pro194_Ser195insTer Pathogenic ★★ same type
- ABCC2 p.Pro274fs 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/abcc2-p-ile1320fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown