Incidental Mutation 'R5845:Vdr'
ID 453584
Institutional Source Beutler Lab
Gene Symbol Vdr
Ensembl Gene ENSMUSG00000022479
Gene Name vitamin D (1,25-dihydroxyvitamin D3) receptor
Synonyms Nr1i1
MMRRC Submission 044063-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5845 (G1)
Quality Score 196
Status Validated
Chromosome 15
Chromosomal Location 97752308-97806177 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 97767647 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Aspartic acid at position 114 (E114D)
Ref Sequence ENSEMBL: ENSMUSP00000023119 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023119]
AlphaFold P48281
Predicted Effect possibly damaging
Transcript: ENSMUST00000023119
AA Change: E114D

PolyPhen 2 Score 0.463 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000023119
Gene: ENSMUSG00000022479
AA Change: E114D

DomainStartEndE-ValueType
ZnF_C4 21 92 1.4e-34 SMART
low complexity region 102 114 N/A INTRINSIC
low complexity region 173 182 N/A INTRINSIC
HOLI 227 389 3.54e-36 SMART
Meta Mutation Damage Score 0.0793 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.1%
  • 20x: 90.3%
Validation Efficiency 97% (59/61)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the nuclear hormone receptor for vitamin D3. This receptor also functions as a receptor for the secondary bile acid lithocholic acid. The receptor belongs to the family of trans-acting transcriptional regulatory factors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets of this nuclear hormone receptor are principally involved in mineral metabolism though the receptor regulates a variety of other metabolic pathways, such as those involved in the 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. Alternative splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Feb 2011]
PHENOTYPE: Homozygous null mutants fail to thrive after weaning and may exhibit excess mortality. Postweaning mutant mice develop alopecia, hypocalcemia, infertility, and rickets. Mutant females exhibit uterine hypoplasia with impaired follicular development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad10 A T 5: 121,764,146 (GRCm39) Y928N probably benign Het
Amz2 T C 11: 109,324,755 (GRCm39) F213S probably damaging Het
Cage1 T A 13: 38,199,682 (GRCm39) S732C probably damaging Het
Ccnf C A 17: 24,459,767 (GRCm39) D229Y possibly damaging Het
Cdon G T 9: 35,368,762 (GRCm39) C332F probably damaging Het
Clca3b G A 3: 144,531,077 (GRCm39) R758C possibly damaging Het
Cyp2ab1 C T 16: 20,131,082 (GRCm39) R349H probably benign Het
Dock10 C T 1: 80,483,459 (GRCm39) probably benign Het
Dock5 A T 14: 68,078,550 (GRCm39) Y225N possibly damaging Het
Ear2 G A 14: 44,340,618 (GRCm39) R92K probably benign Het
Eif3c T C 7: 126,163,927 (GRCm39) S39G probably damaging Het
Eml3 A G 19: 8,916,582 (GRCm39) D701G probably damaging Het
Fat3 G A 9: 16,288,506 (GRCm39) T339I probably damaging Het
Fbn2 T C 18: 58,186,840 (GRCm39) D1687G possibly damaging Het
Fcnb C T 2: 27,969,633 (GRCm39) probably null Het
Flacc1 T A 1: 58,706,937 (GRCm39) E243D possibly damaging Het
Fscb A G 12: 64,519,558 (GRCm39) V636A unknown Het
Gm6124 A G 7: 38,869,299 (GRCm39) noncoding transcript Het
Hectd4 T A 5: 121,445,587 (GRCm39) probably null Het
Hrnr A T 3: 93,239,944 (GRCm39) H3394L unknown Het
Hs1bp3 A G 12: 8,386,275 (GRCm39) R226G probably benign Het
Ifngr2 T C 16: 91,351,947 (GRCm39) V61A probably benign Het
Irag2 G A 6: 145,117,392 (GRCm39) M376I probably benign Het
Kcnk2 T C 1: 189,009,918 (GRCm39) probably benign Het
Kmt2d G A 15: 98,749,990 (GRCm39) probably benign Het
Mgam T A 6: 40,652,257 (GRCm39) N810K possibly damaging Het
Mis18a A G 16: 90,518,522 (GRCm39) probably null Het
Nsmce3 A G 7: 64,521,936 (GRCm39) V244A possibly damaging Het
Or10ag59 T C 2: 87,406,367 (GRCm39) I313T probably benign Het
Plxna4 A T 6: 32,214,711 (GRCm39) V590D probably damaging Het
Prkab1 A T 5: 116,162,219 (GRCm39) D30E probably benign Het
Rasgrp3 A T 17: 75,810,142 (GRCm39) N281Y possibly damaging Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Septin2 T A 1: 93,426,757 (GRCm39) probably null Het
Slc26a6 T G 9: 108,739,282 (GRCm39) V609G possibly damaging Het
Spta1 T A 1: 174,068,662 (GRCm39) M2154K probably damaging Het
Stoml2 T G 4: 43,030,008 (GRCm39) probably benign Het
Sult6b1 A C 17: 79,202,059 (GRCm39) S148A probably damaging Het
Tmem131l A G 3: 83,847,860 (GRCm39) V335A probably damaging Het
Tmem221 T A 8: 72,007,788 (GRCm39) probably null Het
Tmem88 C G 11: 69,288,504 (GRCm39) Q138H probably benign Het
Trpm8 T C 1: 88,255,902 (GRCm39) Y186H probably benign Het
Trpv1 T C 11: 73,131,407 (GRCm39) I7T probably damaging Het
Ttc34 T C 4: 154,949,929 (GRCm39) S961P probably benign Het
Ubr1 T C 2: 120,734,486 (GRCm39) D1138G probably benign Het
Ubr7 C T 12: 102,732,571 (GRCm39) R188C probably damaging Het
Uspl1 C T 5: 149,130,770 (GRCm39) P118S probably benign Het
Zfp853 C T 5: 143,274,424 (GRCm39) V399M unknown Het
Zswim4 T A 8: 84,943,871 (GRCm39) probably null Het
Other mutations in Vdr
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Vdr APN 15 97,782,735 (GRCm39) missense probably damaging 1.00
IGL02813:Vdr APN 15 97,767,562 (GRCm39) missense probably benign 0.45
leftist UTSW 15 97,765,052 (GRCm39) missense probably damaging 1.00
yangshuo UTSW 15 97,757,002 (GRCm39) missense probably damaging 1.00
R0400:Vdr UTSW 15 97,767,232 (GRCm39) missense probably benign 0.00
R1102:Vdr UTSW 15 97,757,002 (GRCm39) missense probably damaging 1.00
R1172:Vdr UTSW 15 97,767,214 (GRCm39) missense probably benign 0.05
R1173:Vdr UTSW 15 97,767,214 (GRCm39) missense probably benign 0.05
R1268:Vdr UTSW 15 97,755,356 (GRCm39) missense probably benign 0.39
R1705:Vdr UTSW 15 97,765,052 (GRCm39) missense probably damaging 1.00
R2879:Vdr UTSW 15 97,757,008 (GRCm39) missense probably benign 0.01
R3030:Vdr UTSW 15 97,755,444 (GRCm39) missense probably benign 0.00
R4695:Vdr UTSW 15 97,756,801 (GRCm39) splice site probably null
R5074:Vdr UTSW 15 97,755,459 (GRCm39) missense probably benign 0.35
R5710:Vdr UTSW 15 97,765,089 (GRCm39) missense probably benign 0.02
R5710:Vdr UTSW 15 97,757,008 (GRCm39) missense probably damaging 1.00
R5982:Vdr UTSW 15 97,755,477 (GRCm39) missense probably benign 0.37
R6776:Vdr UTSW 15 97,767,709 (GRCm39) missense probably damaging 1.00
R6865:Vdr UTSW 15 97,755,386 (GRCm39) missense probably damaging 1.00
R7870:Vdr UTSW 15 97,782,771 (GRCm39) missense possibly damaging 0.59
R9036:Vdr UTSW 15 97,765,089 (GRCm39) missense probably benign 0.03
R9110:Vdr UTSW 15 97,782,753 (GRCm39) missense probably damaging 0.98
R9114:Vdr UTSW 15 97,765,136 (GRCm39) missense probably benign
R9214:Vdr UTSW 15 97,767,600 (GRCm39) missense probably benign 0.01
R9381:Vdr UTSW 15 97,755,333 (GRCm39) missense probably damaging 1.00
R9684:Vdr UTSW 15 97,767,285 (GRCm39) missense probably benign
X0023:Vdr UTSW 15 97,767,699 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGCCTGGGCTATACCTGATTC -3'
(R):5'- ACCGGGTTGTCTCCATGATAAG -3'

Sequencing Primer
(F):5'- GGGCTATACCTGATTCTCCACTAG -3'
(R):5'- TGTCTCCATGATAAGGCATCGGC -3'
Posted On 2017-02-10