VLDLR p.Arg613=
c.1839C>T · rs2488736457 · VCV3009194
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -0.85 | GERP -2.8, phastCons 0.004 |
| Overall | ||
| CADD | 9.773 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,020 alleles
Overall
6.2e-05%
1/1,614,158 alleles · very rare
exomes 1/1,461,856 · genomes 0/152,302 · joint denominator
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.Arg613=
- Coding
- c.1839C>T
- MANE Select
- NM_003383
- dbSNP
- rs2488736457
- Type
- single nucleotide variant
- Location
- chr9:2648224 (GRCh38)
- Gene constraint
- LOEUF 0.828 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.12 · 27 PDB
- Residue 613
- a UniProt-annotated variant site (in)
Similar variants
- VLDLR p.Arg613His Uncertain significance ★★ ⚠ same residue
- 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
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-arg613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown