ABCG8 p.Phe399=
c.1197T>C · rs2466273080 · VCV2123789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -3.6 | GERP -2.9 |
| Overall | ||
| CADD | 0.562 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ABCG8
- Protein
- p.Phe399=
- Coding
- c.1197T>C
- MANE Select
- NM_022437
- dbSNP
- rs2466273080
- Type
- single nucleotide variant
- Location
- chr2:43872292 (GRCh38)
- Gene constraint
- LOEUF 1.329 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.94 · 8 PDB
- Residue 399
- an α-helix
Similar variants
- ABCG8 c.64-2A>G Pathogenic ★★ same type
- ABCG8 c.964+1G>T Likely pathogenic ★★ same type
- ABCG8 c.965-1G>C Pathogenic ★★ same type
- ABCG8 p.Arg121Ter Pathogenic ★★ same type
- ABCG8 p.Arg164Ter Pathogenic ★★ same type
- ABCG8 p.Arg405Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- ABCG8 p.Arg412Ter Pathogenic/Likely pathogenic ★★ same type
- ABCG8 p.Gln271Ter Pathogenic/Likely 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/abcg8-p-phe399 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown