Incidental Mutation 'IGL02141:Rara'
ID281562
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Rara
Ensembl Gene ENSMUSG00000037992
Gene Nameretinoic acid receptor, alpha
SynonymsRAR alpha 1, RARalpha1
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL02141
Quality Score
Status
Chromosome11
Chromosomal Location98927818-98974942 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 98968081 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Asparagine at position 119 (Y119N)
Ref Sequence ENSEMBL: ENSMUSP00000103097 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068133] [ENSMUST00000107473] [ENSMUST00000107474] [ENSMUST00000107475] [ENSMUST00000164748]
Predicted Effect probably damaging
Transcript: ENSMUST00000068133
AA Change: Y122N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: Y122N

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000107473
AA Change: Y119N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: Y119N

DomainStartEndE-ValueType
low complexity region 54 77 N/A INTRINSIC
ZnF_C4 82 153 7.53e-40 SMART
HOLI 227 385 1.22e-34 SMART
low complexity region 422 433 N/A INTRINSIC
low complexity region 436 459 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000107474
AA Change: Y122N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: Y122N

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000107475
AA Change: Y122N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: Y122N

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000164748
AA Change: Y122N

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: Y122N

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 65 80 N/A INTRINSIC
ZnF_C4 85 156 7.53e-40 SMART
HOLI 230 388 1.22e-34 SMART
low complexity region 425 436 N/A INTRINSIC
low complexity region 439 462 N/A INTRINSIC
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for targeted null mutations show high neonatal mortality due to maternal cannibalization, failure to thrive, and excess mortality during the postnatal period. Male survivors exhibit testicular degeneration. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J03Rik C T 5: 146,183,465 A188T probably benign Het
2310022B05Rik A T 8: 124,637,906 probably benign Het
4931423N10Rik T C 2: 23,230,200 F203L probably damaging Het
Arntl2 T A 6: 146,828,095 probably benign Het
Atf6b C A 17: 34,653,277 H539Q probably benign Het
Bpifb5 G T 2: 154,229,557 probably null Het
Cep89 T A 7: 35,420,924 M377K probably damaging Het
Clpx G T 9: 65,312,118 probably null Het
Cops5 T C 1: 10,035,117 K47E probably damaging Het
Cryba2 T C 1: 74,892,784 N35S probably benign Het
Ddx27 A G 2: 167,020,523 K162E possibly damaging Het
Dhx36 A G 3: 62,493,889 S319P probably benign Het
Dram2 A G 3: 106,571,696 probably benign Het
Eci2 T A 13: 34,978,673 T300S probably benign Het
Egf C A 3: 129,739,982 G70* probably null Het
Eif5b T C 1: 38,032,322 V444A probably benign Het
Elf3 T C 1: 135,257,707 D23G possibly damaging Het
Epb41l4b A T 4: 57,103,422 probably null Het
Fam167a T A 14: 63,452,259 S2T probably benign Het
Flrt3 A G 2: 140,660,688 V340A probably damaging Het
Gimap3 T C 6: 48,765,378 E206G probably benign Het
Gp6 T C 7: 4,394,104 probably benign Het
Gpr158 A T 2: 21,783,290 M581L probably damaging Het
Hapln3 A G 7: 79,118,145 V167A probably damaging Het
Hnrnpll G A 17: 80,050,713 T203I probably benign Het
Ighv3-6 A G 12: 114,288,362 I47T probably damaging Het
Iqgap1 G A 7: 80,738,121 T926M probably damaging Het
Lonp1 A T 17: 56,615,086 S765T probably benign Het
Lpp C T 16: 24,761,615 S27F probably damaging Het
Lrit2 T C 14: 37,068,074 probably benign Het
Luc7l C A 17: 26,253,080 T17K probably damaging Het
Mroh1 G T 15: 76,446,599 S1161I possibly damaging Het
Muc5b T G 7: 141,853,367 C1091G unknown Het
Mut A G 17: 40,938,817 T228A possibly damaging Het
Nppb A T 4: 147,986,006 I11F probably benign Het
Nsf A T 11: 103,828,525 D650E probably benign Het
Ogdh A G 11: 6,355,015 K907E probably damaging Het
Olfr1351 A G 10: 79,017,721 Y133C probably damaging Het
Olfr344 A G 2: 36,568,808 D70G probably damaging Het
Olfr362 G A 2: 37,105,425 S75F probably benign Het
Pcnx A T 12: 81,860,382 Q4L possibly damaging Het
Pgc T A 17: 47,726,931 L9H probably damaging Het
Pikfyve T A 1: 65,246,397 S887T probably benign Het
Plec T C 15: 76,175,615 D3239G probably damaging Het
Pole4 T C 6: 82,648,034 T116A probably benign Het
Prpf8 A G 11: 75,490,672 N300D possibly damaging Het
Rbck1 G T 2: 152,318,374 R462S possibly damaging Het
Setdb2 C T 14: 59,402,315 R709Q probably damaging Het
Slfn2 C A 11: 83,069,844 N216K probably benign Het
Suox A G 10: 128,672,098 probably benign Het
Tars T A 15: 11,391,194 Y283F probably damaging Het
Trpm4 A T 7: 45,318,179 probably null Het
Ubtd2 A T 11: 32,499,262 K36N probably benign Het
Unkl T C 17: 25,229,434 L327P probably damaging Het
Vmn1r11 T A 6: 57,137,379 Y9* probably null Het
Vps13b T C 15: 35,572,081 V948A probably benign Het
Zbtb17 A G 4: 141,464,953 H403R probably damaging Het
Other mutations in Rara
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00951:Rara APN 11 98968166 missense probably benign 0.00
IGL01155:Rara APN 11 98968184 missense possibly damaging 0.92
IGL03194:Rara APN 11 98971664 missense possibly damaging 0.96
PIT4486001:Rara UTSW 11 98973495 missense possibly damaging 0.88
R0626:Rara UTSW 11 98971580 critical splice acceptor site probably null
R1973:Rara UTSW 11 98971670 missense possibly damaging 0.91
R3975:Rara UTSW 11 98970569 missense probably damaging 1.00
R4357:Rara UTSW 11 98968111 missense probably damaging 0.98
R5102:Rara UTSW 11 98966359 missense possibly damaging 0.80
R5147:Rara UTSW 11 98950724 missense probably benign 0.35
R5381:Rara UTSW 11 98971584 missense possibly damaging 0.93
R5570:Rara UTSW 11 98972652 missense probably damaging 1.00
R5861:Rara UTSW 11 98968161 nonsense probably null
R6273:Rara UTSW 11 98970222 missense probably benign 0.00
R6404:Rara UTSW 11 98961013 missense probably benign 0.16
Posted On2015-04-16