Incidental Mutation 'R7100:Nr1d1'
ID 550777
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 045192-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7100 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 98658758-98666159 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 98662160 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 158 (R158L)
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

DomainStartEndE-ValueType
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: R158L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000069505
Gene: ENSMUSG00000020889
AA Change: R158L

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
ZnF_C4 50 123 3.09e-36 SMART
HOLI 220 378 2.36e-32 SMART
Meta Mutation Damage Score 0.7826 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 98% (54/55)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl10 A G 2: 154,394,315 (GRCm39) E89G probably damaging Het
Adgrv1 A T 13: 81,419,016 (GRCm39) V5993E probably damaging Het
Amdhd1 T C 10: 93,372,936 (GRCm39) probably null Het
Amph T C 13: 19,334,011 (GRCm39) *691Q probably null Het
Ankrd55 A G 13: 112,492,644 (GRCm39) K272E probably benign Het
Arhgef10l C T 4: 140,244,126 (GRCm39) V838I possibly damaging Het
Arl2 C A 19: 6,184,774 (GRCm39) V160F probably benign Het
Catsperb T C 12: 101,412,297 (GRCm39) V128A possibly damaging Het
Cdk11b T A 4: 155,710,050 (GRCm39) L17H probably damaging Het
Cpsf1 A T 15: 76,480,314 (GRCm39) N1391K possibly damaging Het
Cpxm2 C T 7: 131,656,544 (GRCm39) A573T probably benign Het
Cspg4b T A 13: 113,455,501 (GRCm39) F516I Het
Daxx T C 17: 34,130,416 (GRCm39) S144P probably damaging Het
Dpp3 T C 19: 4,968,069 (GRCm39) D303G probably damaging Het
Fam181a T A 12: 103,282,132 (GRCm39) N12K probably damaging Het
Flg2 A T 3: 93,111,018 (GRCm39) R1015S unknown Het
Fstl5 A G 3: 76,443,600 (GRCm39) H315R probably benign Het
Fut4 A G 9: 14,662,689 (GRCm39) S202P probably damaging Het
Gm5114 T C 7: 39,057,708 (GRCm39) D637G possibly damaging Het
Gstcd G T 3: 132,790,704 (GRCm39) T21K probably benign Het
Heca C T 10: 17,791,121 (GRCm39) V312M probably benign Het
Herpud1 A G 8: 95,117,475 (GRCm39) R144G probably damaging Het
Hycc2 T A 1: 58,573,653 (GRCm39) T384S possibly damaging Het
Ino80 A G 2: 119,204,994 (GRCm39) S1511P possibly damaging Het
Irf2bp2 T C 8: 127,318,472 (GRCm39) T365A probably benign Het
Klk1 G A 7: 43,878,848 (GRCm39) G214E probably damaging Het
Lama3 A T 18: 12,715,701 (GRCm39) N1719I possibly damaging Het
Lmna A G 3: 88,392,297 (GRCm39) I365T probably damaging Het
Lrp8 C A 4: 107,659,647 (GRCm39) A13E possibly damaging Het
Ly75 A G 2: 60,136,778 (GRCm39) L1483P probably benign Het
Maco1 T C 4: 134,533,971 (GRCm39) D550G probably damaging Het
Mid1 A G X: 168,768,073 (GRCm39) D407G probably benign Het
Mpl G T 4: 118,314,607 (GRCm39) A21E Het
Mus81 C T 19: 5,534,239 (GRCm39) G360S probably damaging Het
Nmt2 T A 2: 3,313,950 (GRCm39) S250T probably benign Het
Pcgf6 G A 19: 47,039,153 (GRCm39) P36S unknown Het
Pcnx2 G A 8: 126,485,853 (GRCm39) A1915V probably benign Het
Peak1 A G 9: 56,166,677 (GRCm39) V417A probably damaging Het
Phf20l1 A G 15: 66,476,689 (GRCm39) N262S probably benign Het
Plaat5 T A 19: 7,616,923 (GRCm39) F313I unknown Het
Ppp2r5d A G 17: 46,996,608 (GRCm39) V355A probably benign Het
Rasa3 T C 8: 13,636,897 (GRCm39) T395A probably benign Het
Rims1 T A 1: 22,416,697 (GRCm39) I432F probably benign Het
Rnf123 C T 9: 107,933,838 (GRCm39) C1080Y probably damaging Het
Serpina3g T C 12: 104,204,570 (GRCm39) probably benign Het
Shank2 T A 7: 143,964,901 (GRCm39) D836E possibly damaging Het
Slc24a5 A C 2: 124,922,591 (GRCm39) S118R probably damaging Het
Smg1 G T 7: 117,783,743 (GRCm39) H1048N unknown Het
Specc1l T G 10: 75,081,329 (GRCm39) S242A probably benign Het
Tagap1 A T 17: 7,224,111 (GRCm39) L195Q possibly damaging Het
Trpc3 C A 3: 36,704,216 (GRCm39) E580D probably benign Het
Ttn A T 2: 76,541,166 (GRCm39) V33940E probably benign Het
Upp2 G T 2: 58,681,817 (GRCm39) R318L probably benign Het
Vezt T A 10: 93,832,795 (GRCm39) E205D probably benign Het
Vmn1r177 A G 7: 23,565,535 (GRCm39) F114L probably benign Het
Vmn2r53 C A 7: 12,315,513 (GRCm39) E769* probably null Het
Vnn3 T C 10: 23,741,840 (GRCm39) Y382H probably damaging Het
Other mutations in Nr1d1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R4342:Nr1d1 UTSW 11 98,662,640 (GRCm39) missense probably damaging 1.00
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
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'- TTCTTAAACGGAGGGATTAAGGC -3'
(R):5'- GCTGAATGGCATGGTGCTAC -3'

Sequencing Primer
(F):5'- CTTAAACGGAGGGATTAAGGCAGAAG -3'
(R):5'- AATGGCATGGTGCTACTGTGTAAG -3'
Posted On 2019-05-15