VDR p.Glu311=
c.933G>A · rs150775215 · VCV708021
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 0.39 | GERP -0.39, phastCons 0.99 |
| Overall | ||
| CADD | 10.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 1.39% | 72 |
| European (non-Finnish)grpmax | 0.314% | 318 |
| Remaining individualsnot grpmax-eligible | 0.181% | 553 |
| South Asian | 0.0561% | 1,783 |
| Admixed American | 0.0376% | 2,659 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0347% | 2,881 |
| African / African-American | 0.0244% | 4,105 |
| East Asian | 0.00236% | 42,328 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- VDR
- Protein
- p.Glu311=
- Coding
- c.933G>A
- MANE Select
- NM_000376
- dbSNP
- rs150775215
- Type
- single nucleotide variant
- Location
- chr12:47846426 (GRCh38)
- Gene constraint
- LOEUF 0.714 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.56 · 52 PDB
- Residue 311
- the nr lbd domain; a UniProt-annotated variant site (in vddr2a; loss of calcitriol receptor activity; loss of affinity for calcitriol; no effect on ligand-independent localization to the nucleus); an α-helix
Disease context
vitamin D-dependent rickets, type 2A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hypocalcemic vitamin D-resistant rickets (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- VDR p.Glu311Asp Uncertain significance ★ ⚠ same residue
- VDR p.Arg274His Pathogenic/Likely pathogenic ★★ same condition
- VDR p.Arg30Ter Pathogenic ★★ same condition
- VDR p.Arg343Cys Likely pathogenic ★★ same condition
- VDR p.Arg391His Pathogenic ★★ same condition
- VDR p.Arg50Ter Pathogenic ★★ same condition
- VDR p.Arg73Gln Pathogenic/Likely pathogenic ★★ same condition
- VDR p.Arg73Ter 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/vdr-p-glu311 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown