Incidental Mutation 'R1839:Thra'
ID 205624
Institutional Source Beutler Lab
Gene Symbol Thra
Ensembl Gene ENSMUSG00000058756
Gene Name thyroid hormone receptor alpha
Synonyms Rvr, T3Ralpha, Nr1a1, Thra1, Erba, T3R[a], 6430529J03Rik, TR alpha 2, c-erbAalpha, Thra2, TR alpha 1
MMRRC Submission 045015-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.914) question?
Stock # R1839 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 98631539-98659832 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98646969 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 30 (N30S)
Ref Sequence ENSEMBL: ENSMUSP00000099428 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064187] [ENSMUST00000103139] [ENSMUST00000124072] [ENSMUST00000153043]
AlphaFold P63058
Predicted Effect probably benign
Transcript: ENSMUST00000064187
AA Change: N30S

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756
AA Change: N30S

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 benign
Transcript: ENSMUST00000103139
AA Change: N30S

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: N30S

DomainStartEndE-ValueType
ZnF_C4 50 123 3.09e-36 SMART
HOLI 220 378 7.26e-33 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000124072
AA Change: N30S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756
AA Change: N30S

DomainStartEndE-ValueType
ZnF_C4 50 123 3.09e-36 SMART
HOLI 220 378 2.36e-32 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124130
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142944
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150693
Predicted Effect probably benign
Transcript: ENSMUST00000153043
AA Change: N30S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153468
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152195
Meta Mutation Damage Score 0.0740 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.7%
  • 10x: 94.7%
  • 20x: 90.6%
Validation Efficiency 98% (90/92)
MGI Phenotype FUNCTION: The protein encoded by this gene is one of several nuclear hormone receptors that bind thyroid hormones such as triiodothyronine and thyroxine with high affinity. The encoded protein is a transcription factor that can activate or repress transcription. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mutations in this gene result in diverse phenotypes depending on the location and severity of the mutation. Observed phenotypes may include alterations in thyroid physiology, intestinal remodeling, cerebellum development, bone growth, cardiac function, thermogenesis, and fertility. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 84 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700006A11Rik T C 3: 124,203,369 (GRCm39) T403A probably damaging Het
Acat3 T A 17: 13,147,493 (GRCm39) R175* probably null Het
Adam1b C A 5: 121,639,104 (GRCm39) C647F probably damaging Het
Adam28 T C 14: 68,876,659 (GRCm39) N197S possibly damaging Het
Adcy2 C T 13: 68,837,380 (GRCm39) probably null Het
Adcy5 A T 16: 35,069,310 (GRCm39) N426I probably damaging Het
Adgre1 T C 17: 57,748,299 (GRCm39) S500P probably benign Het
Aloxe3 A G 11: 69,020,911 (GRCm39) Y212C probably damaging Het
Ap3d1 A G 10: 80,562,942 (GRCm39) S180P probably damaging Het
Arhgap20 C T 9: 51,760,626 (GRCm39) R790W probably damaging Het
Atp8b4 C A 2: 126,203,702 (GRCm39) A757S possibly damaging Het
Begain G A 12: 109,001,249 (GRCm39) probably benign Het
Ccdc141 T C 2: 76,842,009 (GRCm39) E1474G probably benign Het
Ccdc88b A G 19: 6,831,477 (GRCm39) probably benign Het
Ccnk A G 12: 108,161,333 (GRCm39) T195A probably damaging Het
Cd55b C A 1: 130,341,842 (GRCm39) C265F probably damaging Het
Celsr3 A G 9: 108,707,105 (GRCm39) H1196R probably benign Het
Cenpt T C 8: 106,575,646 (GRCm39) S190G possibly damaging Het
Chd8 T C 14: 52,442,340 (GRCm39) S2077G probably benign Het
Col6a5 G A 9: 105,742,032 (GRCm39) H2296Y probably benign Het
Cxxc4 C A 3: 133,946,414 (GRCm39) H332N probably damaging Het
Cyp24a1 T C 2: 170,338,661 (GRCm39) I12V probably benign Het
Cyp3a57 T A 5: 145,318,111 (GRCm39) L364Q probably damaging Het
Ddi2 T C 4: 141,440,837 (GRCm39) I47V probably benign Het
Ddx5 A T 11: 106,675,723 (GRCm39) D322E probably benign Het
Dhx40 A G 11: 86,680,123 (GRCm39) C405R possibly damaging Het
Emc1 T C 4: 139,087,796 (GRCm39) F100S probably damaging Het
Exoc2 T C 13: 31,090,480 (GRCm39) probably benign Het
Gm10110 A T 14: 90,135,272 (GRCm39) noncoding transcript Het
Gm17332 T C 11: 31,132,386 (GRCm39) H26R possibly damaging Het
Gna12 T C 5: 140,748,367 (GRCm39) N183S probably benign Het
Gpx6 A G 13: 21,496,497 (GRCm39) N24D probably benign Het
Gsdma3 C T 11: 98,520,684 (GRCm39) A105V probably benign Het
Hsd3b5 T C 3: 98,527,044 (GRCm39) Y134C probably benign Het
Ifi213 T C 1: 173,417,166 (GRCm39) I415M probably damaging Het
Ints9 C A 14: 65,253,979 (GRCm39) P278T probably damaging Het
Krt79 C T 15: 101,846,373 (GRCm39) E192K possibly damaging Het
Lrrk2 A G 15: 91,567,337 (GRCm39) N132S probably benign Het
Ltn1 T A 16: 87,213,152 (GRCm39) K470* probably null Het
Magi2 A T 5: 20,670,825 (GRCm39) T163S probably damaging Het
Mcm9 A G 10: 53,417,649 (GRCm39) M18T probably damaging Het
Med12l A G 3: 58,975,740 (GRCm39) T212A probably benign Het
Mfhas1 T C 8: 36,058,012 (GRCm39) L829P possibly damaging Het
Mgme1 T A 2: 144,121,407 (GRCm39) C288S probably benign Het
Muc4 G C 16: 32,753,919 (GRCm38) R1265P probably benign Het
Myh7 T C 14: 55,210,637 (GRCm39) N1725S possibly damaging Het
Naa80 G A 9: 107,460,216 (GRCm39) R37H possibly damaging Het
Nme4 A T 17: 26,311,071 (GRCm39) W165R probably damaging Het
Nup205 T A 6: 35,196,649 (GRCm39) D1128E probably benign Het
Or2t48 A T 11: 58,420,199 (GRCm39) Y204* probably null Het
Or5ae2 T C 7: 84,505,756 (GRCm39) Y60H probably damaging Het
Pcdh1 T C 18: 38,332,538 (GRCm39) D155G possibly damaging Het
Pex12 A T 11: 83,188,648 (GRCm39) S116T probably damaging Het
Plekhh1 C T 12: 79,125,731 (GRCm39) probably benign Het
Plekhh3 A G 11: 101,054,426 (GRCm39) probably benign Het
Pnpt1 T C 11: 29,104,342 (GRCm39) M572T possibly damaging Het
Ppp1r12b T C 1: 134,765,719 (GRCm39) R667G probably benign Het
Rbpms2 ACTGCTGCTGCTGCTGC ACTGCTGCTGCTGCTGCTGC 9: 65,558,948 (GRCm39) probably benign Het
Rgs14 T C 13: 55,530,651 (GRCm39) probably benign Het
Rhbdf2 A T 11: 116,491,017 (GRCm39) V645E possibly damaging Het
Robo3 A G 9: 37,333,623 (GRCm39) V696A probably benign Het
Sall1 A G 8: 89,755,344 (GRCm39) F1212L possibly damaging Het
Sdc4 T C 2: 164,270,932 (GRCm39) E109G probably benign Het
Serpind1 G T 16: 17,160,856 (GRCm39) R462L probably damaging Het
Smad9 CTTT CTT 3: 54,696,600 (GRCm39) probably benign Het
Sstr4 C A 2: 148,237,453 (GRCm39) N21K probably benign Het
Tap1 C T 17: 34,407,083 (GRCm39) A77V possibly damaging Het
Thap4 T C 1: 93,678,009 (GRCm39) E259G probably benign Het
Tmem207 A T 16: 26,343,571 (GRCm39) V27E possibly damaging Het
Top3a A G 11: 60,644,714 (GRCm39) V305A probably damaging Het
Trim59 A T 3: 68,944,971 (GRCm39) I123K probably damaging Het
Ttn T C 2: 76,691,839 (GRCm39) probably benign Het
Ubac1 T A 2: 25,897,750 (GRCm39) E290V possibly damaging Het
Unc13b T C 4: 43,258,308 (GRCm39) probably benign Het
Uri1 A T 7: 37,666,814 (GRCm39) D206E probably benign Het
Utp4 A G 8: 107,640,086 (GRCm39) H465R probably benign Het
Uvssa T C 5: 33,547,096 (GRCm39) S221P probably benign Het
Vmn1r39 T C 6: 66,782,217 (GRCm39) probably null Het
Vps39 A T 2: 120,155,878 (GRCm39) L514H probably damaging Het
Vps72 G A 3: 95,026,529 (GRCm39) R158Q possibly damaging Het
Wdr59 T C 8: 112,211,972 (GRCm39) D366G probably benign Het
Zfp366 C A 13: 99,365,000 (GRCm39) Q54K probably damaging Het
Zfp523 T A 17: 28,413,967 (GRCm39) I34N probably damaging Het
Zfp974 G A 7: 27,609,781 (GRCm39) P648L possibly damaging Het
Other mutations in Thra
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01021:Thra APN 11 98,653,754 (GRCm39) missense possibly damaging 0.90
IGL01544:Thra APN 11 98,647,754 (GRCm39) missense possibly damaging 0.46
IGL02377:Thra APN 11 98,652,742 (GRCm39) missense probably damaging 1.00
IGL02738:Thra APN 11 98,655,185 (GRCm39) missense probably benign 0.40
IGL03111:Thra APN 11 98,651,855 (GRCm39) unclassified probably benign
California UTSW 11 98,655,134 (GRCm39) missense probably damaging 0.97
Crissal UTSW 11 98,653,777 (GRCm39) missense probably benign 0.20
R0033_Thra_272 UTSW 11 98,655,178 (GRCm39) missense probably benign 0.00
R0033:Thra UTSW 11 98,655,178 (GRCm39) missense probably benign 0.00
R0033:Thra UTSW 11 98,655,178 (GRCm39) missense probably benign 0.00
R0959:Thra UTSW 11 98,644,455 (GRCm39) missense possibly damaging 0.94
R1659:Thra UTSW 11 98,647,805 (GRCm39) missense probably damaging 0.99
R1859:Thra UTSW 11 98,646,977 (GRCm39) missense probably damaging 0.98
R1935:Thra UTSW 11 98,653,899 (GRCm39) splice site probably benign
R1956:Thra UTSW 11 98,654,567 (GRCm39) missense probably benign 0.03
R4584:Thra UTSW 11 98,655,310 (GRCm39) missense probably benign 0.42
R4782:Thra UTSW 11 98,646,990 (GRCm39) missense probably benign 0.01
R5414:Thra UTSW 11 98,651,783 (GRCm39) missense probably benign 0.34
R5790:Thra UTSW 11 98,653,777 (GRCm39) missense probably benign 0.20
R5927:Thra UTSW 11 98,654,514 (GRCm39) missense possibly damaging 0.56
R7207:Thra UTSW 11 98,651,802 (GRCm39) missense probably damaging 1.00
R7234:Thra UTSW 11 98,654,544 (GRCm39) missense probably damaging 1.00
R7307:Thra UTSW 11 98,655,134 (GRCm39) missense probably damaging 0.97
R7825:Thra UTSW 11 98,653,774 (GRCm39) missense probably benign 0.14
R7875:Thra UTSW 11 98,659,257 (GRCm39) missense probably damaging 0.98
R8385:Thra UTSW 11 98,659,177 (GRCm39) missense probably benign 0.40
R8669:Thra UTSW 11 98,654,476 (GRCm39) missense possibly damaging 0.89
R8955:Thra UTSW 11 98,644,449 (GRCm39) missense possibly damaging 0.92
R9549:Thra UTSW 11 98,653,772 (GRCm39) missense probably benign 0.14
R9615:Thra UTSW 11 98,651,715 (GRCm39) missense probably damaging 1.00
Z1177:Thra UTSW 11 98,644,307 (GRCm39) start gained probably benign
Predicted Primers PCR Primer
(F):5'- GACCCTTTCCAAGCTTTGTCAG -3'
(R):5'- TCCTCCTCAAAGGCCAGAATAG -3'

Sequencing Primer
(F):5'- GCTTTGTCAGCTGATATAGGGG -3'
(R):5'- CTCCTCAAAGGCCAGAATAGGTTTTG -3'
Posted On 2014-06-23