ABCG5 p.Val439=
c.1317G>C · VCV3311104
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Cardiovascular phenotype
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 -0.094, phastCons 1 |
| Overall | ||
| CADD | 9.804 | 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
- ABCG5
- Protein
- p.Val439=
- Coding
- c.1317G>C
- MANE Select
- NM_022436
- Type
- single nucleotide variant
- Location
- chr2:43823920 (GRCh38)
- Gene constraint
- LOEUF 1.219 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.48 · 8 PDB
- Residue 439
- the abc transmembrane type-2 domain; an α-helix
Similar variants
- ABCG5 c.1325-1G>T Likely pathogenic ★★ same condition
- ABCG5 p.Gln251Ter Pathogenic ★★ same condition
- ABCG5 p.Glu146Ter Pathogenic ★★ same condition
- ABCG5 p.Ala170Asp Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala264Val Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala278Glu Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala333Ser Uncertain significance ★★ ⚠ same condition
- ABCG5 p.Ala429Thr Uncertain significance ★★ ⚠ 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/abcg5-p-val439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown