Mutagenetix > Incidental Mutation

Incidental Mutation 'R9381:Vdr'

710064

Institutional Source

Beutler Lab

Gene Symbol

Vdr

Ensembl Gene

ENSMUSG00000022479

Gene Name

vitamin D (1,25-dihydroxyvitamin D3) receptor

Synonyms

Nr1i1

MMRRC Submission

068992-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9381 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

97752308-97806177 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 97755333 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 397 (R397C)

Ref Sequence

ENSEMBL: ENSMUSP00000023119 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023119]

AlphaFold

P48281

Predicted Effect

probably damaging
Transcript: ENSMUST00000023119
AA Change: R397C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000023119
Gene: ENSMUSG00000022479
AA Change: R397C

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2200002D01Rik	CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC	CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC	7: 28,947,048 (GRCm39)		probably benign	Het
9930111J21Rik1	T	A	11: 48,839,204 (GRCm39)	K461M	probably damaging	Het
Abhd16b	A	G	2: 181,135,881 (GRCm39)	Y261C	probably damaging	Het
Acadl	T	C	1: 66,893,805 (GRCm39)	T117A	probably benign	Het
Adamts15	A	G	9: 30,813,816 (GRCm39)	V783A	probably damaging	Het
Aff1	A	T	5: 103,981,733 (GRCm39)	Q624L	possibly damaging	Het
Afg3l2	T	G	18: 67,575,451 (GRCm39)	E74A	probably damaging	Het
Aig1	T	C	10: 13,523,417 (GRCm39)	E238G	probably benign	Het
Ankrd17	C	T	5: 90,416,508 (GRCm39)	R1108Q	probably damaging	Het
Anks1	A	T	17: 28,272,979 (GRCm39)	Y958F	probably damaging	Het
Arhgef28	C	A	13: 98,036,269 (GRCm39)	Q1663H	possibly damaging	Het
Asb3	T	C	11: 31,051,088 (GRCm39)	L475P	probably damaging	Het
Atg9a	T	A	1: 75,162,726 (GRCm39)	M430L	probably benign	Het
Bco1	T	A	8: 117,837,631 (GRCm39)	V164E	probably benign	Het
Bhlhe40	T	C	6: 108,642,244 (GRCm39)	L396P	probably damaging	Het
C5ar2	A	T	7: 15,970,887 (GRCm39)	S347T	probably damaging	Het
Cdc42bpa	T	C	1: 179,969,048 (GRCm39)	S1212P	probably damaging	Het
Ceacam3	C	G	7: 16,893,715 (GRCm39)	Q409E		Het
Ces3b	T	C	8: 105,811,670 (GRCm39)	V62A	probably benign	Het
Dalrd3	A	G	9: 108,448,242 (GRCm39)		probably null	Het
Ddhd2	G	T	8: 26,239,849 (GRCm39)	A288E	probably benign	Het
Dnah17	T	A	11: 117,914,219 (GRCm39)	M4435L	probably benign	Het
Dok1	T	C	6: 83,009,972 (GRCm39)	K46E	probably damaging	Het
E030025P04Rik	A	G	11: 109,030,384 (GRCm39)	Y168H	unknown	Het
Elavl2	T	C	4: 91,197,009 (GRCm39)	N23S	probably benign	Het
Elfn1	T	C	5: 139,959,462 (GRCm39)	V822A	probably damaging	Het
Emb	G	T	13: 117,357,096 (GRCm39)		probably benign	Het
Exoc5	C	T	14: 49,275,194 (GRCm39)	S202N	probably benign	Het
Fryl	T	C	5: 73,240,637 (GRCm39)	D1321G	probably benign	Het
Gm12258	C	T	11: 58,750,007 (GRCm39)	T394I	unknown	Het
Gm28363	T	A	1: 117,654,615 (GRCm39)	S85T	probably damaging	Het
H2-Q1	A	G	17: 35,542,138 (GRCm39)	T237A	probably damaging	Het
Hectd4	A	T	5: 121,472,492 (GRCm39)	I2743F	possibly damaging	Het
Hs3st3b1	C	T	11: 63,812,692 (GRCm39)	G8S	probably benign	Het
Ighv1-16	T	C	12: 114,629,598 (GRCm39)	N63S	probably benign	Het
Il20rb	A	G	9: 100,343,541 (GRCm39)	F238L	possibly damaging	Het
Il31ra	A	T	13: 112,668,253 (GRCm39)	F439I	possibly damaging	Het
Jup	C	T	11: 100,270,391 (GRCm39)	C372Y	probably damaging	Het
Kat2a	T	C	11: 100,602,692 (GRCm39)	Q132R	possibly damaging	Het
Kcnq2	A	G	2: 180,751,562 (GRCm39)	I278T	probably damaging	Het
Lama1	T	C	17: 68,044,479 (GRCm39)	V126A		Het
Lama2	T	A	10: 27,064,023 (GRCm39)	R1285*	probably null	Het
Larp1	A	G	11: 57,949,532 (GRCm39)	T1054A	probably benign	Het
Lrp1	A	T	10: 127,441,337 (GRCm39)	M262K	probably benign	Het
Lrrd1	A	G	5: 3,901,074 (GRCm39)	I460V	probably benign	Het
Ltbp1	A	T	17: 75,696,434 (GRCm39)	N1606I	probably damaging	Het
Mdga2	T	C	12: 66,597,304 (GRCm39)	N730S	possibly damaging	Het
Mpzl1	T	C	1: 165,429,323 (GRCm39)	H236R	probably damaging	Het
Mrps31	G	A	8: 22,904,752 (GRCm39)	R47K	probably damaging	Het
Nae1	A	T	8: 105,250,239 (GRCm39)	I218K	probably benign	Het
Npy2r	T	C	3: 82,448,356 (GRCm39)	T140A	probably damaging	Het
Nr2e1	T	A	10: 42,439,468 (GRCm39)	L350F	probably damaging	Het
Nup210l	C	T	3: 90,107,173 (GRCm39)	P1570L	probably benign	Het
Or51d1	A	T	7: 102,347,654 (GRCm39)	M70L	probably damaging	Het
Or5b124	G	T	19: 13,610,647 (GRCm39)	M57I	probably damaging	Het
Or5p50	A	C	7: 107,421,812 (GRCm39)	L288W	probably damaging	Het
Pabpc1l	G	T	2: 163,867,423 (GRCm39)	C8F	probably benign	Het
Pafah1b3	A	C	7: 24,994,699 (GRCm39)	F172V	probably benign	Het
Pcdhga6	A	T	18: 37,841,371 (GRCm39)	T364S	probably damaging	Het
Ppp3cc	T	A	14: 70,462,441 (GRCm39)	M399L	probably benign	Het
Prpsap2	T	C	11: 61,635,782 (GRCm39)	I173V	probably benign	Het
Rabggtb	A	T	3: 153,613,817 (GRCm39)	W252R	probably damaging	Het
Raph1	A	G	1: 60,540,959 (GRCm39)	F351L	unknown	Het
Rasd2	T	C	8: 75,948,589 (GRCm39)	S172P	probably damaging	Het
Rbm15	T	C	3: 107,238,752 (GRCm39)	T549A	probably benign	Het
Reln	A	G	5: 22,549,202 (GRCm39)	Y69H	possibly damaging	Het
Samd3	T	A	10: 26,147,643 (GRCm39)	N439K	probably benign	Het
Scap	C	A	9: 110,207,839 (GRCm39)	A516D	probably damaging	Het
Selplg	T	C	5: 113,957,917 (GRCm39)	T130A	probably benign	Het
Slc12a7	A	G	13: 73,949,063 (GRCm39)	M697V	probably benign	Het
Slc22a29	A	G	19: 8,195,841 (GRCm39)	I66T	probably benign	Het
Slco1a7	T	C	6: 141,711,490 (GRCm39)	I74V	probably benign	Het
Snrnp48	A	C	13: 38,404,667 (GRCm39)	I241L	probably damaging	Het
Sptb	C	T	12: 76,634,292 (GRCm39)	E2140K	probably benign	Het
Strip2	T	C	6: 29,927,333 (GRCm39)	S192P	probably benign	Het
Svil	A	T	18: 5,099,013 (GRCm39)	R1643S	probably benign	Het
Tbc1d2b	A	G	9: 90,101,139 (GRCm39)	V617A	possibly damaging	Het
Tmem102	T	C	11: 69,695,141 (GRCm39)	E277G	probably benign	Het
Tmtc4	T	G	14: 123,163,441 (GRCm39)	I648L	probably benign	Het
Togaram1	T	C	12: 65,014,204 (GRCm39)	V485A	probably damaging	Het
Trim43b	T	C	9: 88,969,642 (GRCm39)	I269V	probably benign	Het
Trpm2	T	A	10: 77,747,191 (GRCm39)	I1436F	possibly damaging	Het
Ube2d3	A	T	3: 135,168,722 (GRCm39)	I106F	possibly damaging	Het
Vps50	T	C	6: 3,592,433 (GRCm39)	S689P	probably benign	Het
Wipf2	A	G	11: 98,787,068 (GRCm39)	T366A	probably damaging	Het
Zfp128	T	C	7: 12,624,897 (GRCm39)	Y422H	possibly damaging	Het
Zfyve28	G	A	5: 34,373,932 (GRCm39)	T694I	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
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
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
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'- CTGCAGTCTACAGGAAAGGG -3'
(R):5'- GGTACAGGATGCTAAGCTGG -3'

Sequencing Primer
(F):5'- CTGCAGTCTACAGGAAAGGGAGATC -3'
(R):5'- CTAAGCTGGTTGAAGCCATTCAG -3'

Posted On

2022-04-18