Incidental Mutation 'IGL02141:Rara'
ID 281562
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Rara
Ensembl Gene ENSMUSG00000037992
Gene Name retinoic acid receptor, alpha
Synonyms RARalpha1, RAR alpha 1
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02141
Quality Score
Status
Chromosome 11
Chromosomal Location 98818644-98865768 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 98858907 bp (GRCm39)
Zygosity Heterozygous
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]
AlphaFold P11416
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: 146,120,275 (GRCm39) A188T probably benign Het
2310022B05Rik A T 8: 125,364,645 (GRCm39) probably benign Het
Atf6b C A 17: 34,872,251 (GRCm39) H539Q probably benign Het
Bmal2 T A 6: 146,729,593 (GRCm39) probably benign Het
Bpifb5 G T 2: 154,071,477 (GRCm39) probably null Het
Cep89 T A 7: 35,120,349 (GRCm39) M377K probably damaging Het
Clpx G T 9: 65,219,400 (GRCm39) probably null Het
Cops5 T C 1: 10,105,342 (GRCm39) K47E probably damaging Het
Cryba2 T C 1: 74,931,943 (GRCm39) N35S probably benign Het
Ddx27 A G 2: 166,862,443 (GRCm39) K162E possibly damaging Het
Dhx36 A G 3: 62,401,310 (GRCm39) S319P probably benign Het
Dram2 A G 3: 106,479,012 (GRCm39) probably benign Het
Eci2 T A 13: 35,162,656 (GRCm39) T300S probably benign Het
Egf C A 3: 129,533,631 (GRCm39) G70* probably null Het
Eif5b T C 1: 38,071,403 (GRCm39) V444A probably benign Het
Elf3 T C 1: 135,185,445 (GRCm39) D23G possibly damaging Het
Epb41l4b A T 4: 57,103,422 (GRCm39) probably null Het
Fam167a T A 14: 63,689,708 (GRCm39) S2T probably benign Het
Flrt3 A G 2: 140,502,608 (GRCm39) V340A probably damaging Het
Gimap3 T C 6: 48,742,312 (GRCm39) E206G probably benign Het
Gp6 T C 7: 4,397,103 (GRCm39) probably benign Het
Gpr158 A T 2: 21,788,101 (GRCm39) M581L probably damaging Het
Hapln3 A G 7: 78,767,893 (GRCm39) V167A probably damaging Het
Hnrnpll G A 17: 80,358,142 (GRCm39) T203I probably benign Het
Ighv3-6 A G 12: 114,251,982 (GRCm39) I47T probably damaging Het
Iqgap1 G A 7: 80,387,869 (GRCm39) T926M probably damaging Het
Lonp1 A T 17: 56,922,086 (GRCm39) S765T probably benign Het
Lpp C T 16: 24,580,365 (GRCm39) S27F probably damaging Het
Lrit2 T C 14: 36,790,031 (GRCm39) probably benign Het
Luc7l C A 17: 26,472,054 (GRCm39) T17K probably damaging Het
Mmut A G 17: 41,249,708 (GRCm39) T228A possibly damaging Het
Mroh1 G T 15: 76,330,799 (GRCm39) S1161I possibly damaging Het
Muc5b T G 7: 141,407,104 (GRCm39) C1091G unknown Het
Nppb A T 4: 148,070,463 (GRCm39) I11F probably benign Het
Nsf A T 11: 103,719,351 (GRCm39) D650E probably benign Het
Ogdh A G 11: 6,305,015 (GRCm39) K907E probably damaging Het
Or1b1 G A 2: 36,995,437 (GRCm39) S75F probably benign Het
Or1j15 A G 2: 36,458,820 (GRCm39) D70G probably damaging Het
Or7a35 A G 10: 78,853,555 (GRCm39) Y133C probably damaging Het
Pcnx1 A T 12: 81,907,156 (GRCm39) Q4L possibly damaging Het
Pgc T A 17: 48,037,856 (GRCm39) L9H probably damaging Het
Pikfyve T A 1: 65,285,556 (GRCm39) S887T probably benign Het
Plec T C 15: 76,059,815 (GRCm39) D3239G probably damaging Het
Pole4 T C 6: 82,625,015 (GRCm39) T116A probably benign Het
Potegl T C 2: 23,120,212 (GRCm39) F203L probably damaging Het
Prpf8 A G 11: 75,381,498 (GRCm39) N300D possibly damaging Het
Rbck1 G T 2: 152,160,294 (GRCm39) R462S possibly damaging Het
Setdb2 C T 14: 59,639,764 (GRCm39) R709Q probably damaging Het
Slfn2 C A 11: 82,960,670 (GRCm39) N216K probably benign Het
Suox A G 10: 128,507,967 (GRCm39) probably benign Het
Tars1 T A 15: 11,391,280 (GRCm39) Y283F probably damaging Het
Trpm4 A T 7: 44,967,603 (GRCm39) probably null Het
Ubtd2 A T 11: 32,449,262 (GRCm39) K36N probably benign Het
Unkl T C 17: 25,448,408 (GRCm39) L327P probably damaging Het
Vmn1r11 T A 6: 57,114,364 (GRCm39) Y9* probably null Het
Vps13b T C 15: 35,572,227 (GRCm39) V948A probably benign Het
Zbtb17 A G 4: 141,192,264 (GRCm39) H403R probably damaging Het
Other mutations in Rara
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00951:Rara APN 11 98,858,992 (GRCm39) missense probably benign 0.00
IGL01155:Rara APN 11 98,859,010 (GRCm39) missense possibly damaging 0.92
IGL03194:Rara APN 11 98,862,490 (GRCm39) missense possibly damaging 0.96
annie UTSW 11 98,864,452 (GRCm39) missense unknown
kane UTSW 11 98,862,595 (GRCm39) missense probably damaging 1.00
Orphan UTSW 11 98,860,989 (GRCm39) missense probably damaging 1.00
warbucks UTSW 11 98,861,395 (GRCm39) missense probably damaging 1.00
PIT4486001:Rara UTSW 11 98,864,321 (GRCm39) missense possibly damaging 0.88
R0626:Rara UTSW 11 98,862,406 (GRCm39) critical splice acceptor site probably null
R1973:Rara UTSW 11 98,862,496 (GRCm39) missense possibly damaging 0.91
R3975:Rara UTSW 11 98,861,395 (GRCm39) missense probably damaging 1.00
R4357:Rara UTSW 11 98,858,937 (GRCm39) missense probably damaging 0.98
R5102:Rara UTSW 11 98,857,185 (GRCm39) missense possibly damaging 0.80
R5147:Rara UTSW 11 98,841,550 (GRCm39) missense probably benign 0.35
R5381:Rara UTSW 11 98,862,410 (GRCm39) missense possibly damaging 0.93
R5570:Rara UTSW 11 98,863,478 (GRCm39) missense probably damaging 1.00
R5861:Rara UTSW 11 98,858,987 (GRCm39) nonsense probably null
R6273:Rara UTSW 11 98,861,048 (GRCm39) missense probably benign 0.00
R6404:Rara UTSW 11 98,851,839 (GRCm39) missense probably benign 0.16
R8906:Rara UTSW 11 98,860,989 (GRCm39) missense probably damaging 1.00
R8921:Rara UTSW 11 98,864,452 (GRCm39) missense unknown
R8978:Rara UTSW 11 98,862,595 (GRCm39) missense probably damaging 1.00
R9224:Rara UTSW 11 98,857,236 (GRCm39) frame shift probably null
R9476:Rara UTSW 11 98,860,983 (GRCm39) missense probably benign 0.02
R9510:Rara UTSW 11 98,860,983 (GRCm39) missense probably benign 0.02
Posted On 2015-04-16