Incidental Mutation 'R2879:Vdr'
ID 260252
Institutional Source Beutler Lab
Gene Symbol Vdr
Ensembl Gene ENSMUSG00000022479
Gene Name vitamin D (1,25-dihydroxyvitamin D3) receptor
Synonyms Nr1i1
MMRRC Submission 040467-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2879 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 97752308-97806177 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 97757008 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 288 (Y288F)
Ref Sequence ENSEMBL: ENSMUSP00000023119 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023119]
AlphaFold P48281
Predicted Effect probably benign
Transcript: ENSMUST00000023119
AA Change: Y288F

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000023119
Gene: ENSMUSG00000022479
AA Change: Y288F

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139656
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 G C 17: 24,508,481 (GRCm39) T1018R probably damaging Het
Acte1 T A 7: 143,447,800 (GRCm39) Y214* probably null Het
Akap9 A G 5: 4,026,353 (GRCm39) probably benign Het
Ankrd29 G A 18: 12,387,757 (GRCm39) A275V possibly damaging Het
Ano6 T A 15: 95,841,308 (GRCm39) C468* probably null Het
Arhgef10l G T 4: 140,242,598 (GRCm39) H890Q probably benign Het
Ccnj T A 19: 40,833,158 (GRCm39) L112Q probably damaging Het
Chaf1a T C 17: 56,351,114 (GRCm39) probably null Het
Chchd4 A G 6: 91,442,200 (GRCm39) S73P probably damaging Het
Chd3 T C 11: 69,254,924 (GRCm39) K139E possibly damaging Het
Cyp2b13 T G 7: 25,785,456 (GRCm39) probably null Het
Dagla T C 19: 10,248,448 (GRCm39) I71V possibly damaging Het
Epor A T 9: 21,870,936 (GRCm39) W315R probably damaging Het
Etv1 T A 12: 38,833,809 (GRCm39) probably null Het
Fbn2 A T 18: 58,202,314 (GRCm39) C1280S probably damaging Het
Fbxo2 G C 4: 148,250,468 (GRCm39) R269P probably damaging Het
Fer1l4 A T 2: 155,894,120 (GRCm39) L61Q probably damaging Het
Ggnbp2 C T 11: 84,723,797 (GRCm39) probably null Het
Grm7 G T 6: 110,623,309 (GRCm39) V161F probably damaging Het
Ibsp G A 5: 104,458,260 (GRCm39) E266K possibly damaging Het
Lamb3 T A 1: 193,013,092 (GRCm39) M439K possibly damaging Het
Lnx1 C T 5: 74,780,784 (GRCm39) V246M probably benign Het
Lrrc32 A G 7: 98,148,984 (GRCm39) Q588R probably benign Het
Magi2 A AG 5: 20,807,459 (GRCm39) probably null Het
Med13 C T 11: 86,189,988 (GRCm39) A974T possibly damaging Het
Mogat2 A T 7: 98,871,573 (GRCm39) I246N possibly damaging Het
Myl2 T C 5: 122,242,748 (GRCm39) probably null Het
Obscn T C 11: 59,022,472 (GRCm39) R758G possibly damaging Het
Or1p1c T A 11: 74,161,049 (GRCm39) V278D probably damaging Het
Osbpl8 T A 10: 111,105,297 (GRCm39) S251T probably benign Het
Pik3r2 A G 8: 71,225,029 (GRCm39) Y145H probably benign Het
Plg A G 17: 12,622,987 (GRCm39) E509G possibly damaging Het
Pnkp T A 7: 44,508,102 (GRCm39) S142T probably damaging Het
Ros1 C T 10: 52,048,936 (GRCm39) probably null Het
Sbno1 A G 5: 124,526,635 (GRCm39) M960T probably damaging Het
Smad1 T C 8: 80,080,084 (GRCm39) probably null Het
Ssc5d G A 7: 4,939,906 (GRCm39) probably null Het
Tfcp2 C T 15: 100,449,201 (GRCm39) probably null Het
Tmem121 A G 12: 113,152,028 (GRCm39) Y82C probably damaging Het
Tmem131 T C 1: 36,880,788 (GRCm39) I161V possibly damaging Het
Tpp2 T A 1: 44,010,783 (GRCm39) F523L probably damaging Het
Ttn C T 2: 76,601,849 (GRCm39) silent Het
Ttpal A G 2: 163,457,503 (GRCm39) probably null Het
Wipf2 C T 11: 98,783,480 (GRCm39) A302V probably benign Het
Zfp346 T G 13: 55,253,163 (GRCm39) C3G possibly damaging 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
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
R5845:Vdr UTSW 15 97,767,647 (GRCm39) missense possibly damaging 0.46
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'- TATGAGGGGTTCGATCAGCTC -3'
(R):5'- GTTGCCTGAGACTTGAACCAG -3'

Sequencing Primer
(F):5'- TGAGGTAGAGACATCCACCCG -3'
(R):5'- CTGAGACTTGAACCAGTTACCTG -3'
Posted On 2015-01-23