ABCG1 p.Phe574=
c.1722C>T · rs139692028 · VCV3044829
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.37%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -3.7 |
| Overall | ||
| CADD | 7.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.37%
East Asian · 613/44,882 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0393%
635/1,614,194 alleles · low-frequency
exomes 579/1,461,870 · genomes 56/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.37% | 73 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,907 |
| South Asian | 0.0022% | 45,542 |
| European (non-Finnish) | 0.000339% | 295,004 |
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.Phe574=
- Coding
- c.1722C>T
- MANE Select
- NM_016818
- dbSNP
- rs139692028
- Type
- single nucleotide variant
- Location
- chr21:42294610 (GRCh38)
- Gene constraint
- LOEUF 0.573 · pLI 0.20 (gnomAD)
- Structure
- AlphaFold pLDDT 81.34 · 5 PDB
- Residue 574
- the abc transmembrane type-2 domain; an α-helix
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.Leu113= 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-phe574 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown