Incidental Mutation 'IGL03194:Rara'
ID412736
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 #IGL03194
Quality Score
Status
Chromosome11
Chromosomal Location98927818-98974942 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 98971664 bp
ZygosityHeterozygous
Amino Acid Change Methionine to Threonine at position 297 (M297T)
Ref Sequence ENSEMBL: ENSMUSP00000129791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068133] [ENSMUST00000107473] [ENSMUST00000107474] [ENSMUST00000107475] [ENSMUST00000164748]
Predicted Effect possibly damaging
Transcript: ENSMUST00000068133
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: M297T

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 possibly damaging
Transcript: ENSMUST00000107473
AA Change: M294T

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: M294T

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 possibly damaging
Transcript: ENSMUST00000107474
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: M297T

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 possibly damaging
Transcript: ENSMUST00000107475
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: M297T

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 possibly damaging
Transcript: ENSMUST00000164748
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: M297T

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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgre5 T C 8: 83,734,018 S64G possibly damaging Het
Clcn7 T C 17: 25,150,548 V306A probably damaging Het
Clec4b2 G A 6: 123,200,987 G87D probably benign Het
Disp2 A T 2: 118,787,629 R219W probably damaging Het
Dstyk A T 1: 132,456,316 probably benign Het
F830045P16Rik T C 2: 129,460,320 S451G possibly damaging Het
Fam155a T C 8: 9,232,975 D358G probably damaging Het
Fat2 T A 11: 55,310,995 T418S probably benign Het
Fto G A 8: 91,409,787 D228N probably damaging Het
Gins4 A T 8: 23,234,746 probably benign Het
Gm10220 T A 5: 26,121,233 R40W probably damaging Het
Gm11149 G A 9: 49,546,346 probably benign Het
Gm5431 T G 11: 48,895,537 probably benign Het
Hebp1 A G 6: 135,155,192 M59T probably benign Het
Lrp1 A T 10: 127,568,685 V1989D probably damaging Het
Lrrc6 A T 15: 66,442,199 D317E probably benign Het
Ltc4s T C 11: 50,236,571 *151W probably null Het
Map3k21 A G 8: 125,924,062 T268A possibly damaging Het
Mdp1 A G 14: 55,658,987 L164P probably damaging Het
Mroh4 T C 15: 74,611,539 T650A probably damaging Het
Mss51 T C 14: 20,485,097 N202D probably benign Het
Mtus2 G A 5: 148,107,103 A834T probably damaging Het
Ncoa6 A G 2: 155,415,868 M585T possibly damaging Het
Nelfcd G A 2: 174,426,832 A559T possibly damaging Het
Npvf A C 6: 50,650,898 D180E possibly damaging Het
Nup188 A T 2: 30,304,334 Y173F possibly damaging Het
Oas3 C A 5: 120,758,953 A868S probably damaging Het
Pkhd1l1 A G 15: 44,518,135 T1086A probably damaging Het
Pla2g6 G A 15: 79,317,785 P62L probably damaging Het
Tmc1 T C 19: 20,804,653 E567G probably damaging Het
Tnxb C T 17: 34,695,947 Q1970* probably null Het
Usp11 T C X: 20,712,417 I162T probably benign Het
Utrn A G 10: 12,406,429 probably benign Het
Zfhx3 A G 8: 108,794,727 E827G 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
IGL02141:Rara APN 11 98968081 missense probably damaging 1.00
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 On2016-08-02