ABCC2 p.Leu76del
c.223CTT[1] · VCV3606975
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -5.1 |
| Overall | ||
| CADD | 19.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,926 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00031%
5/1,613,904 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,732 |
| European (non-Finnish) | 8.48e-05% | 1,179,920 |
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.Leu76del
- Coding
- c.223CTT[1]
- MANE Select
- NM_000392
- Type
- Microsatellite
- Location
- chr10:99792247 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 76
- an α-helix
Similar variants
- ABCC2 p.Glu1405del Uncertain significance ★★ same type
- ABCC2 p.Ala364fs Pathogenic ★ same type
- ABCC2 p.Ile799fs Pathogenic ★ same type
- ABCC2 p.Thr912_Leu913insTer Pathogenic ★ same type
- ABCC2 p.Tyr776fs Pathogenic ★ same type
- ABCC2 p.Val1197fs Pathogenic ★ same type
- ABCC2 c.2620+10_2620+12del Conflicting classifications of pathogenicity ★ same type
- ABCC2 p.Ile1380_Pro1381insIle Uncertain significance ★ 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-leu76del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown