Incidental Mutation 'R1268:Vdr'
| ID |
151224 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vdr
|
| Ensembl Gene |
ENSMUSG00000022479 |
| Gene Name |
vitamin D (1,25-dihydroxyvitamin D3) receptor |
| Synonyms |
Nr1i1 |
| MMRRC Submission |
039335-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R1268 (G1)
|
| Quality Score |
215 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
97752308-97806177 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 97755356 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 389
(N389S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000023119
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023119]
|
| AlphaFold |
P48281 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000023119
AA Change: N389S
PolyPhen 2
Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000023119
Gene: ENSMUSG00000022479
AA Change: N389S
| Domain | Start | End | E-Value | Type |
|---|
|
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
|
| Meta Mutation Damage Score |
0.1111 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.7%
- 20x: 93.6%
|
| Validation Efficiency |
100% (41/41) |
| 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: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Afdn |
T |
C |
17: 14,108,248 (GRCm39) |
V1257A |
probably damaging |
Het |
| Aplnr |
A |
G |
2: 84,967,775 (GRCm39) |
T267A |
possibly damaging |
Het |
| Arap2 |
A |
G |
5: 62,887,964 (GRCm39) |
S461P |
probably benign |
Het |
| Brpf3 |
A |
G |
17: 29,055,530 (GRCm39) |
T1160A |
probably damaging |
Het |
| Col5a1 |
A |
T |
2: 27,892,501 (GRCm39) |
T1005S |
unknown |
Het |
| Crebrf |
CTTTT |
CTTT |
17: 26,958,570 (GRCm39) |
|
probably null |
Het |
| Fmo6 |
A |
T |
1: 162,748,086 (GRCm39) |
I326N |
probably damaging |
Het |
| Foxp4 |
G |
C |
17: 48,191,278 (GRCm39) |
|
probably benign |
Het |
| Gnat1 |
A |
G |
9: 107,553,076 (GRCm39) |
|
probably benign |
Het |
| Hs6st1 |
T |
A |
1: 36,108,007 (GRCm39) |
V90D |
probably damaging |
Het |
| Igsf11 |
A |
G |
16: 38,845,216 (GRCm39) |
T257A |
probably benign |
Het |
| Ints2 |
C |
T |
11: 86,123,911 (GRCm39) |
G626R |
probably damaging |
Het |
| Mab21l3 |
C |
T |
3: 101,742,363 (GRCm39) |
E66K |
possibly damaging |
Het |
| Mroh2a |
C |
T |
1: 88,158,402 (GRCm39) |
R150* |
probably null |
Het |
| Mybl2 |
A |
G |
2: 162,916,636 (GRCm39) |
N429S |
probably benign |
Het |
| Mycbp2 |
G |
A |
14: 103,446,218 (GRCm39) |
T1837I |
probably damaging |
Het |
| Myh7b |
C |
A |
2: 155,455,966 (GRCm39) |
S117* |
probably null |
Het |
| Nek1 |
C |
A |
8: 61,475,298 (GRCm39) |
A202E |
probably damaging |
Het |
| Notum |
C |
T |
11: 120,549,493 (GRCm39) |
W159* |
probably null |
Het |
| Ntn1 |
TCCTCGGC |
TC |
11: 68,103,959 (GRCm39) |
|
probably benign |
Het |
| Nup58 |
A |
T |
14: 60,482,119 (GRCm39) |
|
probably benign |
Het |
| Or2w2 |
C |
T |
13: 21,758,498 (GRCm39) |
V43M |
probably benign |
Het |
| Or4c58 |
A |
G |
2: 89,674,498 (GRCm39) |
I273T |
probably damaging |
Het |
| Or4f57 |
G |
T |
2: 111,791,222 (GRCm39) |
N65K |
possibly damaging |
Het |
| Or5b99 |
T |
C |
19: 12,976,625 (GRCm39) |
Y92H |
possibly damaging |
Het |
| Or5p69 |
A |
T |
7: 107,967,002 (GRCm39) |
I102F |
probably benign |
Het |
| Or7g12 |
T |
C |
9: 18,899,652 (GRCm39) |
F123L |
probably damaging |
Het |
| Plk4 |
T |
A |
3: 40,765,804 (GRCm39) |
V659D |
probably damaging |
Het |
| Rbm27 |
T |
C |
18: 42,466,367 (GRCm39) |
S866P |
probably damaging |
Het |
| Rnaseh2b |
A |
T |
14: 62,609,904 (GRCm39) |
K303N |
possibly damaging |
Het |
| Samd9l |
C |
T |
6: 3,376,113 (GRCm39) |
V383I |
possibly damaging |
Het |
| Shf |
G |
A |
2: 122,199,163 (GRCm39) |
P51S |
probably damaging |
Het |
| Slc35f2 |
T |
A |
9: 53,705,197 (GRCm39) |
Y62* |
probably null |
Het |
| Tenm2 |
C |
T |
11: 35,954,004 (GRCm39) |
G1236R |
possibly damaging |
Het |
| Ulk1 |
A |
G |
5: 110,938,143 (GRCm39) |
S610P |
probably damaging |
Het |
| Ulk4 |
C |
A |
9: 121,086,140 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Vdr |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
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'- GAATGGACTCATCTCTTCTGCCTGC -3'
(R):5'- TTCCATCCTGTGACACAGACCGAC -3'
Sequencing Primer
(F):5'- CAGCAGTGTCTCCTAACTGAG -3'
(R):5'- ACCTGGGGTACAGGATGC -3'
|
| Posted On |
2014-01-29 |
Incidental Mutation