ABCC1 p.Leu855=
c.2565G>T · rs28364004 · VCV775038
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, afr)
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 0.77 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 7.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
African / African-American · 954/75,068 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.11%
1,771/1,613,846 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.27% | 79 |
| Middle Eastern | 0.644% | 155 |
| Admixed American | 0.282% | 355 |
| Ashkenazi Jewishnot grpmax-eligible | 0.216% | 462 |
| Remaining individualsnot grpmax-eligible | 0.186% | 539 |
| European (non-Finnish) | 0.0354% | 2,823 |
| South Asian | 0.0121% | 8,279 |
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
- ABCC1
- Protein
- p.Leu855=
- Coding
- c.2565G>T
- MANE Select
- NM_004996
- dbSNP
- rs28364004
- Type
- single nucleotide variant
- Location
- chr16:16090509 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 5 PDB
- Residue 855
- an α-helix; the abc transporter 1 domain
Similar variants
- ABCC1 p.Thr1464Met Uncertain significance ★★ ⚠ same type
- ABCC1 c.1381-5C>G Benign ★★ same type
- ABCC1 p.Ala1260= Benign ★★ same type
- ABCC1 p.Ala1406= Benign ★★ same type
- ABCC1 p.Arg433Ser Benign ★★ same type
- ABCC1 p.Asp637= Likely benign ★★ same type
- ABCC1 p.Gly762= Benign/Likely benign ★★ same type
- ABCC1 p.Gly885= Benign ★★ 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/abcc1-p-leu855 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown