VLDLR p.Ala798=
c.2394C>T · rs761966145 · VCV2902421
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, mid)
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 -0.048 | GERP -3.4, phastCons 0.9 |
| Overall | ||
| CADD | 8.974 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,060 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00718%
Overall
0.00359%
58/1,614,072 alleles · ultra-rare
exomes 48/1,461,780 · genomes 10/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,020 |
| African / African-American | 0.0107% | 9,379 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| European (non-Finnish) | 0.00347% | 28,780 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
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
- VLDLR
- Protein
- p.Ala798=
- Coding
- c.2394C>T
- MANE Select
- NM_003383
- dbSNP
- rs761966145
- Type
- single nucleotide variant
- Location
- chr9:2651932 (GRCh38)
- Gene constraint
- LOEUF 0.828 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.12 · 27 PDB
Similar variants
- VLDLR c.2252-2A>C Likely pathogenic ★★ same type
- VLDLR c.449-2A>T Likely pathogenic ★★ same type
- VLDLR c.83-1G>A Pathogenic/Likely pathogenic ★★ same type
- VLDLR p.Arg279Ter Pathogenic ★★ same type
- VLDLR p.Arg301Ter Pathogenic ★★ same type
- VLDLR p.Trp529Ter Pathogenic ★★ same type
- VLDLR c.-154C>G Uncertain significance ★★ same type
- VLDLR c.-392C>T Uncertain significance ★★ 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/vldlr-p-ala798 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown