ABCG1 p.Leu113=
c.339G>A · rs2229411 · VCV3060995
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.01%, eas)
Conditions
1
ABCG1-related disorder
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 1.3 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 7.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.01%
East Asian · 1,673/41,768 alleles
Filtering AF
3.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.78%
Overall
0.26%
4,115/1,584,138 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.01% | 25 |
| Admixed American | 3.46% | 29 |
| Remaining individualsnot grpmax-eligible | 0.511% | 196 |
| South Asian | 0.14% | 713 |
| African / African-American | 0.0995% | 1,005 |
| Middle Eastern | 0.05% | 2,001 |
| European (non-Finnish) | 0.00514% | 19,462 |
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
- ABCG1
- Protein
- p.Leu113=
- Coding
- c.339G>A
- MANE Select
- NM_016818
- dbSNP
- rs2229411
- Type
- single nucleotide variant
- Location
- chr21:42271122 (GRCh38)
- Gene constraint
- LOEUF 0.573 · pLI 0.20 (gnomAD)
- Structure
- AlphaFold pLDDT 81.34 · 5 PDB
- Residue 113
- the abc transporter domain
Disease context
ABCG1-related disorder
Similar variants
- ABCG1 p.Phe640Leu Uncertain significance ⚠ same condition
- ABCG1 c.538-6C>T Benign same condition
- ABCG1 p.Ala203= Likely benign same condition
- ABCG1 p.Asp614= Likely benign same condition
- ABCG1 p.Cys3= Benign same condition
- ABCG1 p.Gly331= Benign same condition
- ABCG1 p.Gly358Arg Benign same condition
- ABCG1 p.Phe448= Likely benign 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/abcg1-p-leu113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown