12-47842623-ATTTTTTTTTT-ATTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_000376.3(VDR):c.*2122_*2123insAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00034 ( 0 hom., cov: 0)
Consequence
VDR
NM_000376.3 3_prime_UTR
NM_000376.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.933
Genes affected
VDR (HGNC:12679): (vitamin D receptor) This gene encodes vitamin D3 receptor, which is a member of the nuclear hormone receptor superfamily of ligand-inducible transcription factors. This receptor also functions as a receptor for the secondary bile acid, lithocholic acid. Downstream targets of vitamin D3 receptor are principally involved in mineral metabolism, though this receptor regulates a variety of other metabolic pathways, such as those involved in immune response and cancer. Mutations in this gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiation codon results in an alternate translation start site three codons downstream. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VDR | NM_000376.3 | c.*2122_*2123insAAAAAAAA | 3_prime_UTR_variant | 10/10 | ENST00000549336.6 | NP_000367.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VDR | ENST00000549336.6 | c.*2122_*2123insAAAAAAAA | 3_prime_UTR_variant | 10/10 | 1 | NM_000376.3 | ENSP00000449573 | P1 | ||
VDR | ENST00000395324.6 | c.*2122_*2123insAAAAAAAA | 3_prime_UTR_variant | 10/10 | 5 | ENSP00000378734 | P1 | |||
VDR | ENST00000550325.5 | downstream_gene_variant | 1 | ENSP00000447173 | ||||||
VDR | ENST00000229022.9 | downstream_gene_variant | 5 | ENSP00000229022 |
Frequencies
GnomAD3 genomes AF: 0.000343 AC: 45AN: 131050Hom.: 0 Cov.: 0
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GnomAD4 genome AF: 0.000343 AC: 45AN: 131050Hom.: 0 Cov.: 0 AF XY: 0.000290 AC XY: 18AN XY: 62012
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at