# NM_000376.3(VDR):c.888C>T (p.Arg296=)

https://sugi.bio/variant/vdr-p-arg296

## Summary

**VDR p.Arg296= (c.888C>T)** is classified **Likely benign** in VDR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-14). Very rare (popmax 0.00267%, afr).

**At a glance:** Likely benign · review: Single submitter · rsID rs768711979 · 1 submitter · very rare (popmax 0.00267%, afr)

## For patients & families {#patients}

This is a change in the VDR gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [VDR](https://sugi.bio/atlas/gene/VDR/) |
| Protein change (HGVS p.) | p.Arg296= |
| Coding change (HGVS c.) | c.888C>T |
| MANE Select transcript | [NM_000376](https://www.ncbi.nlm.nih.gov/nuccore/NM_000376) |
| dbSNP | [rs768711979](https://www.ncbi.nlm.nih.gov/snp/rs768711979/) |
| Variant type | single nucleotide variant |
| Location | chr12:47846676-47846676 (GRCh38) |
| ClinVar | [VCV1159663](https://www.ncbi.nlm.nih.gov/clinvar/variation/1159663/) |

**All HGVS expressions:** `NC_000012.11:g.48240459G>A`, `NC_000012.12:g.47846676G>A`, `NG_008731.1:g.63356C>T`, `NM_000376.3:c.888C>T`, `NM_001017535.2:c.888C>T`, `NM_001017536.2:c.1038C>T`, `NM_001364085.2:c.888C>T`, `NM_001374661.1:c.888C>T`, `NM_001374662.1:c.888C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -2.666, GERP -3.46 — fast-evolving / accelerated position
- CADD: **PHRED 0.76**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (G>C, Δ0.59 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00267%** (afr) · FAF95 0.000542% · FAF99 0.000428% · 2/74,908 in the highest group · 16/1,613,786 alleles overall — very rare (popmax 0.00267%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00267% | 37,454 |
| East Asian | 0.00223% | 44,888 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.00102% | 98,338 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**VDR** population constraint: LOEUF 0.714, pLI 0.01086, missense-Z 2.1968. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **296** lies in 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).

AlphaFold model confidence (whole protein): pLDDT 84.56, 74% of residues very-high.

**52 experimental structure(s)** (PDB): [1DB1](https://www.rcsb.org/structure/1DB1), [1IE8](https://www.rcsb.org/structure/1IE8), [1IE9](https://www.rcsb.org/structure/1IE9), [1KB2](https://www.rcsb.org/structure/1KB2), [1KB4](https://www.rcsb.org/structure/1KB4), [1KB6](https://www.rcsb.org/structure/1KB6) — incl. mutant structure 3M7R.

## What this gene does {#gene-function}

*Describes the biological roles of VDR (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** VDR's established molecular role includes DNA binding. p.Arg296= falls in the nr lbd domain.


### Pathways affected {#pathways}

VDR participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Nuclear Receptor transcription pathway](https://reactome.org/content/detail/R-HSA-383280) | curated |
| [SUMOylation of intracellular receptors](https://reactome.org/content/detail/R-HSA-4090294) | curated |
| [Vitamin D (calciferol) metabolism](https://reactome.org/content/detail/R-HSA-196791) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** DNA binding, nuclear receptor activity, bile acid nuclear receptor activity, nuclear retinoid X receptor binding, calcitriol binding, lithocholic acid binding.

**Biological process:** negative regulation of transcription by RNA polymerase II, cell morphogenesis, negative regulation of cell population proliferation, positive regulation of gene expression, negative regulation of keratinocyte proliferation, phosphate ion transmembrane transport.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-04-14.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2023-04-14 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related VDR variant pages (same residue, condition, or type): [VDR p.Arg296Cys](/variant/vdr-p-arg296cys), [VDR p.Arg274His](/variant/vdr-p-arg274his), [VDR p.Arg30Ter](/variant/vdr-p-arg30ter), [VDR p.Arg343Cys](/variant/vdr-p-arg343cys), [VDR p.Arg391His](/variant/vdr-p-arg391his), [VDR p.Arg50Ter](/variant/vdr-p-arg50ter), [VDR p.Arg73Gln](/variant/vdr-p-arg73gln), [VDR p.Arg73Ter](/variant/vdr-p-arg73ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1159663). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*