Mutagenetix > Incidental Mutation

Incidental Mutation 'R4342:Nr1d1'

324187

Institutional Source

Beutler Lab

Gene Symbol

Nr1d1

Ensembl Gene

ENSMUSG00000020889

Gene Name

nuclear receptor subfamily 1, group D, member 1

Synonyms

A530070C09Rik, rev-erbA(alpha), REV-ERBalpha

MMRRC Submission

041100-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4342 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

98658758-98666159 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 98662640 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamine at position 118 (K118Q)

Ref Sequence

ENSEMBL: ENSMUSP00000069505 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000064187] [ENSMUST00000064941] [ENSMUST00000124072]

AlphaFold

Q3UV55

Predicted Effect

probably benign
Transcript: ENSMUST00000064187

SMART Domains

Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756

Domain	Start	End	E-Value	Type
ZnF_C4	50	123	3.09e-36	SMART
HOLI	220	378	1.43e-31	SMART
low complexity region	461	484	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000064941
AA Change: K118Q

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000069505
Gene: ENSMUSG00000020889
AA Change: K118Q

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
low complexity region	70	94	N/A	INTRINSIC
ZnF_C4	130	202	5.54e-38	SMART
low complexity region	240	263	N/A	INTRINSIC
PDB:3N00\|A	282	361	2e-21	PDB
HOLI	442	600	4.2e-38	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000124072

SMART Domains

Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756

Domain	Start	End	E-Value	Type
ZnF_C4	50	123	3.09e-36	SMART
HOLI	220	378	2.36e-32	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139220

Meta Mutation Damage Score

0.1561

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

99% (68/69)

MGI Phenotype

FUNCTION: This gene encodes a transcription factor that is a member of the nuclear receptor subfamily 1. The encoded protein is a ligand-sensitive transcription factor that negatively regulates the expression of core clock proteins. In particular this protein represses the circadian clock transcription factor aryl hydrocarbon receptor nuclear translocator-like protein 1 (Arntl). This protein may also be involved in regulating genes that function in metabolic, inflammatory and cardiovascular processes. [provided by RefSeq, Feb 2014]
PHENOTYPE: Homozygotes for targeted null mutations exhibit altered circadian behavior and temperature regulation with mild alterations in cytoarchitecture of the cerebellum. Litter size is reduced by half in mutant females. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	T	C	17: 45,827,421 (GRCm39)	C488R	probably benign	Het
Adamts19	A	T	18: 59,075,572 (GRCm39)	H489L	probably damaging	Het
Ahnak	T	C	19: 8,989,447 (GRCm39)	V3577A	possibly damaging	Het
Ajm1	A	G	2: 25,469,120 (GRCm39)	Y264H	possibly damaging	Het
Arhgap44	G	A	11: 64,902,887 (GRCm39)	R401*	probably null	Het
Cbx3-ps2	T	C	13: 65,707,502 (GRCm39)		noncoding transcript	Het
Ccdc174	T	A	6: 91,862,337 (GRCm39)	L86*	probably null	Het
Cd38	A	C	5: 44,026,431 (GRCm39)	I72L	probably benign	Het
Cers4	T	C	8: 4,571,223 (GRCm39)	L264P	probably damaging	Het
Cldn23	A	G	8: 36,292,652 (GRCm39)	S279P	probably benign	Het
Cth	T	A	3: 157,630,613 (GRCm39)	T19S	probably damaging	Het
Dnajc22	T	A	15: 99,002,345 (GRCm39)	L330*	probably null	Het
Epas1	G	A	17: 87,131,228 (GRCm39)	C336Y	probably damaging	Het
Evi5l	A	C	8: 4,233,492 (GRCm39)		probably benign	Het
Fbxl2	A	T	9: 113,814,374 (GRCm39)	H272Q	probably benign	Het
Fgd3	C	T	13: 49,427,185 (GRCm39)		probably null	Het
Fhdc1	C	A	3: 84,352,133 (GRCm39)	V1031F	probably benign	Het
Fscn1	T	C	5: 142,957,776 (GRCm39)	Y308H	probably damaging	Het
Garin3	A	G	11: 46,298,043 (GRCm39)	D449G	possibly damaging	Het
Gm5878	G	A	6: 85,102,633 (GRCm39)	R31*	probably null	Het
Gpatch2l	T	C	12: 86,307,453 (GRCm39)	V277A	probably benign	Het
Greb1l	T	A	18: 10,544,561 (GRCm39)	M1385K	probably benign	Het
Grin2a	A	G	16: 9,471,453 (GRCm39)	I605T	possibly damaging	Het
Hoxc11	C	T	15: 102,863,106 (GRCm39)	S49F	probably damaging	Het
Igf2r	C	T	17: 12,928,398 (GRCm39)	E982K	possibly damaging	Het
Ighv10-3	A	T	12: 114,487,124 (GRCm39)	M99K	possibly damaging	Het
Itgb4	A	T	11: 115,879,555 (GRCm39)	T614S	probably benign	Het
Kcnv1	G	A	15: 44,977,840 (GRCm39)	T66M	probably damaging	Het
Mast4	A	G	13: 102,910,756 (GRCm39)	V461A	probably damaging	Het
Mcts2	G	A	2: 152,529,584 (GRCm39)	V132M	probably damaging	Het
Mical3	C	A	6: 120,911,799 (GRCm39)	E1083*	probably null	Het
Nbeal2	A	G	9: 110,460,861 (GRCm39)		probably benign	Het
Nek4	T	C	14: 30,675,863 (GRCm39)	V66A	probably damaging	Het
Nfasc	A	G	1: 132,559,443 (GRCm39)	F229S	probably damaging	Het
Nhsl1	T	C	10: 18,402,437 (GRCm39)	F1221S	probably damaging	Het
Ntaq1	T	C	15: 58,016,110 (GRCm39)	S120P	probably benign	Het
Ntm	T	C	9: 29,020,727 (GRCm39)	E164G	probably damaging	Het
Or51a7	A	G	7: 102,615,231 (GRCm39)	N308S	probably benign	Het
Parp1	G	T	1: 180,414,894 (GRCm39)	A411S	probably benign	Het
Pds5b	A	G	5: 150,724,319 (GRCm39)	T1301A	probably benign	Het
Pkhd1	A	G	1: 20,128,841 (GRCm39)	V3954A	probably benign	Het
Pkp4	A	T	2: 59,180,952 (GRCm39)	K739I	probably damaging	Het
Pla2g4e	T	C	2: 120,016,927 (GRCm39)		probably benign	Het
Plod3	G	C	5: 137,017,000 (GRCm39)	A50P	probably benign	Het
Ralgds	T	C	2: 28,442,107 (GRCm39)	L96P	probably damaging	Het
Rbm6	A	T	9: 107,724,446 (GRCm39)		probably benign	Het
Scp2d1	T	C	2: 144,666,087 (GRCm39)	L142P	probably damaging	Het
Setd5	AT	ATT	6: 113,088,281 (GRCm39)		probably benign	Het
Sgf29	G	A	7: 126,270,949 (GRCm39)	C143Y	probably damaging	Het
Slc22a12	A	G	19: 6,591,129 (GRCm39)	I156T	probably benign	Het
Stambpl1	A	G	19: 34,211,446 (GRCm39)	Q169R	probably benign	Het
Tex2	T	C	11: 106,457,832 (GRCm39)		probably benign	Het
Trip11	A	T	12: 101,850,575 (GRCm39)	I878N	probably damaging	Het
Ttf1	C	T	2: 28,955,488 (GRCm39)	S284L	probably benign	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ugt2b5	A	T	5: 87,287,582 (GRCm39)	V195E	probably damaging	Het
Vmn1r14	T	A	6: 57,210,808 (GRCm39)	Y85N	probably benign	Het
Zfp131	C	T	13: 120,237,554 (GRCm39)	R268H	probably damaging	Het

Other mutations in Nr1d1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0048:Nr1d1	UTSW	11	98,661,304 (GRCm39)	missense	probably benign
R1485:Nr1d1	UTSW	11	98,661,187 (GRCm39)	missense	probably benign
R1801:Nr1d1	UTSW	11	98,662,325 (GRCm39)	missense	probably damaging	1.00
R2090:Nr1d1	UTSW	11	98,661,436 (GRCm39)	missense	probably damaging	0.99
R4622:Nr1d1	UTSW	11	98,660,710 (GRCm39)	missense	probably damaging	1.00
R4658:Nr1d1	UTSW	11	98,662,738 (GRCm39)	missense	possibly damaging	0.80
R4664:Nr1d1	UTSW	11	98,662,086 (GRCm39)	missense	possibly damaging	0.95
R4770:Nr1d1	UTSW	11	98,661,471 (GRCm39)	missense	probably benign	0.28
R5408:Nr1d1	UTSW	11	98,661,087 (GRCm39)	missense	probably benign	0.02
R5677:Nr1d1	UTSW	11	98,662,134 (GRCm39)	missense	probably damaging	1.00
R5713:Nr1d1	UTSW	11	98,661,237 (GRCm39)	missense	probably benign	0.00
R6244:Nr1d1	UTSW	11	98,661,363 (GRCm39)	missense	probably damaging	1.00
R6429:Nr1d1	UTSW	11	98,662,840 (GRCm39)	missense	probably damaging	1.00
R6875:Nr1d1	UTSW	11	98,661,662 (GRCm39)	splice site	probably null
R7073:Nr1d1	UTSW	11	98,662,892 (GRCm39)	missense	probably damaging	0.99
R7100:Nr1d1	UTSW	11	98,662,160 (GRCm39)	missense	probably damaging	1.00
R7900:Nr1d1	UTSW	11	98,660,537 (GRCm39)	missense	probably benign	0.10
R8296:Nr1d1	UTSW	11	98,662,133 (GRCm39)	missense	probably damaging	1.00
R8678:Nr1d1	UTSW	11	98,660,073 (GRCm39)	missense	probably damaging	1.00
R8679:Nr1d1	UTSW	11	98,660,073 (GRCm39)	missense	probably damaging	1.00
R8757:Nr1d1	UTSW	11	98,660,073 (GRCm39)	missense	probably damaging	1.00
R8759:Nr1d1	UTSW	11	98,660,073 (GRCm39)	missense	probably damaging	1.00
R9195:Nr1d1	UTSW	11	98,659,883 (GRCm39)	missense	possibly damaging	0.80
R9715:Nr1d1	UTSW	11	98,662,943 (GRCm39)	missense	probably benign	0.01
R9746:Nr1d1	UTSW	11	98,661,160 (GRCm39)	missense	probably benign
X0018:Nr1d1	UTSW	11	98,661,655 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGGCTCAAGGTTCTAGGAG -3'
(R):5'- TCCCTGACTCAAGGTTGTCC -3'

Sequencing Primer
(F):5'- GCTCTCACGTCTAGGTGACTG -3'
(R):5'- TGACTCAAGGTTGTCCCACATAC -3'

Posted On

2015-06-24