VLDLR p.Asp263=
c.789C>T · rs1300815833 · VCV2882032
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 0.2 | GERP -0.9, phastCons 0.96 |
| Overall | ||
| CADD | 7.534 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,080 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000372%
6/1,614,218 alleles · very rare
exomes 6/1,461,888 · genomes 0/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,770 |
| East Asian | 0.00223% | 44,886 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
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.Asp263=
- Coding
- c.789C>T
- MANE Select
- NM_003383
- dbSNP
- rs1300815833
- Type
- single nucleotide variant
- Location
- chr9:2643500 (GRCh38)
- Gene constraint
- LOEUF 0.828 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.12 · 27 PDB
- Residue 263
- the ldl-receptor class a 6 domain
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-asp263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown