APOB p.Glu1010=
c.3030G>A · rs764325150 · VCV1799039
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
Conditions
3
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 -3.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,179,992 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.00109%
16/1,461,848 alleles · very rare
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
- APOB
- Protein
- p.Glu1010=
- Coding
- c.3030G>A
- MANE Select
- NM_000384
- dbSNP
- rs764325150
- Type
- single nucleotide variant
- Location
- chr2:21019083 (GRCh38)
- Gene constraint
- LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Similar variants
- APOB p.Glu1010Asp Uncertain significance ★ ⚠ same residue
- APOB c.1830-1G>A Pathogenic ★★ same condition
- APOB c.2604+1G>A Likely pathogenic ★★ same condition
- APOB c.537+1G>T Pathogenic/Likely pathogenic ★★ same condition
- APOB p.Arg1333Ter Pathogenic ★★ same condition
- APOB p.Arg2012Ter Pathogenic ★★ same condition
- APOB p.Arg2085Ter Pathogenic/Likely pathogenic ★★ same condition
- APOB p.Arg2513Ter Pathogenic ★★ 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/apob-p-glu1010 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown