Incidental Mutation 'R1859:Thra'
ID 204245
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
Accession Numbers
Essential gene? Probably essential (E-score: 0.914) question?
Stock # R1859 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 98631539-98659832 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 98646977 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 33 (C33S)
Ref Sequence ENSEMBL: ENSMUSP00000099428 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064187] [ENSMUST00000103139] [ENSMUST00000124072] [ENSMUST00000153043]
AlphaFold P63058
Predicted Effect probably damaging
Transcript: ENSMUST00000064187
AA Change: C33S

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756
AA Change: C33S

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: ENSMUST00000103139
AA Change: C33S

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: C33S

DomainStartEndE-ValueType
ZnF_C4 50 123 3.09e-36 SMART
HOLI 220 378 7.26e-33 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000124072
AA Change: C33S

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756
AA Change: C33S

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 possibly damaging
Transcript: ENSMUST00000153043
AA Change: C33S

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153468
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152195
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.3%
Validation Efficiency
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: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001K19Rik C T 12: 110,637,268 (GRCm39) probably benign Het
Adcy10 A G 1: 165,349,530 (GRCm39) E467G probably damaging Het
Alkbh8 A G 9: 3,385,499 (GRCm39) D597G probably benign Het
Alpk1 T A 3: 127,474,749 (GRCm39) H418L possibly damaging Het
Ano5 G T 7: 51,196,581 (GRCm39) V138L probably damaging Het
Aspg T A 12: 112,087,606 (GRCm39) I319K possibly damaging Het
Atp9b T C 18: 80,793,135 (GRCm39) T970A possibly damaging Het
Brd10 A C 19: 29,732,323 (GRCm39) C230G possibly damaging Het
C4b T A 17: 34,954,527 (GRCm39) M881L probably benign Het
Cd209c A T 8: 3,994,953 (GRCm39) N70K probably benign Het
Cdca5 T C 19: 6,140,124 (GRCm39) V95A possibly damaging Het
Cds2 A G 2: 132,144,115 (GRCm39) Y297C probably damaging Het
Celsr2 C T 3: 108,303,946 (GRCm39) G2371S probably damaging Het
Cemip2 T C 19: 21,825,341 (GRCm39) V1213A possibly damaging Het
Chd5 T A 4: 152,464,980 (GRCm39) I1557N probably benign Het
Cntn5 C T 9: 9,972,839 (GRCm39) E266K probably damaging Het
Crtam G A 9: 40,884,900 (GRCm39) T363M possibly damaging Het
Dnah2 A G 11: 69,328,712 (GRCm39) S3298P probably damaging Het
Dok1 A T 6: 83,009,226 (GRCm39) Y209N probably damaging Het
Dpp10 T C 1: 123,281,333 (GRCm39) D561G possibly damaging Het
Drosha A G 15: 12,878,804 (GRCm39) K710R probably benign Het
Dse T C 10: 34,029,225 (GRCm39) T622A probably benign Het
Duxf4 A G 10: 58,071,602 (GRCm39) V204A probably benign Het
Ercc6 T C 14: 32,248,735 (GRCm39) S429P probably damaging Het
Fam135a A T 1: 24,069,306 (GRCm39) V521E probably damaging Het
Fbxl7 A T 15: 26,543,279 (GRCm39) L456Q probably damaging Het
Fbxo38 A G 18: 62,648,489 (GRCm39) I683T probably damaging Het
Foxc2 G T 8: 121,843,364 (GRCm39) R4L probably damaging Het
Glyctk C T 9: 106,034,731 (GRCm39) V112I probably benign Het
Guf1 G T 5: 69,725,803 (GRCm39) G481* probably null Het
Heatr1 T C 13: 12,418,040 (GRCm39) L324S probably damaging Het
Hectd1 A G 12: 51,853,350 (GRCm39) L57P probably damaging Het
Hmcn1 A T 1: 150,532,944 (GRCm39) C3080S probably damaging Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Ifit1 T A 19: 34,624,944 (GRCm39) F27I probably benign Het
Ift20 G T 11: 78,430,860 (GRCm39) E68* probably null Het
Itsn1 A G 16: 91,686,042 (GRCm39) probably benign Het
Ksr2 T A 5: 117,553,006 (GRCm39) L38Q probably damaging Het
Lama2 A T 10: 26,907,078 (GRCm39) M2361K possibly damaging Het
Lrrc56 A G 7: 140,787,421 (GRCm39) M353V probably benign Het
Lsmem1 GTACATACATACATACATACATACATACA GTACATACATACATACATACATACATACATACA 12: 40,235,260 (GRCm39) probably null Het
Map3k9 A T 12: 81,771,256 (GRCm39) S800R possibly damaging Het
Mef2a A G 7: 66,915,766 (GRCm39) S179P probably damaging Het
Micall1 A G 15: 79,007,145 (GRCm39) probably benign Het
Mpg A G 11: 32,181,957 (GRCm39) probably null Het
Mpp7 A T 18: 7,350,967 (GRCm39) *577K probably null Het
Msh4 G T 3: 153,611,517 (GRCm39) H35Q probably benign Het
Mst1 G A 9: 107,961,545 (GRCm39) V601I probably benign Het
Myh10 T A 11: 68,636,239 (GRCm39) N246K probably benign Het
Myom3 C A 4: 135,506,707 (GRCm39) N493K probably benign Het
Mypn T C 10: 62,981,969 (GRCm39) D537G probably benign Het
Ncan A T 8: 70,567,998 (GRCm39) M38K possibly damaging Het
Ndufaf6 G T 4: 11,053,474 (GRCm39) H277Q probably benign Het
Nos1 A T 5: 118,043,527 (GRCm39) N601Y possibly damaging Het
Nrxn2 G A 19: 6,538,825 (GRCm39) V794I probably benign Het
Or10q12 T A 19: 13,746,088 (GRCm39) Y127* probably null Het
Or13a17 T A 7: 140,271,571 (GRCm39) V251E possibly damaging Het
Or13c7b A T 4: 43,820,779 (GRCm39) I194N possibly damaging Het
Or2y17 T C 11: 49,232,211 (GRCm39) L284P probably damaging Het
Or8h9 T C 2: 86,789,425 (GRCm39) I126V probably damaging Het
Parp4 T C 14: 56,886,372 (GRCm39) V1817A unknown Het
Pfdn1 C A 18: 36,584,153 (GRCm39) M60I probably benign Het
Ppp1r3c T C 19: 36,711,011 (GRCm39) N253S probably damaging Het
Prdm5 A G 6: 65,808,263 (GRCm39) I42V probably benign Het
Prom2 T G 2: 127,383,017 (GRCm39) Q75P probably damaging Het
Ptpn23 T C 9: 110,217,938 (GRCm39) D669G possibly damaging Het
Rag1 T C 2: 101,474,407 (GRCm39) D245G probably benign Het
Rpl22l1 T A 3: 28,860,747 (GRCm39) probably null Het
Sars2 T C 7: 28,443,737 (GRCm39) V113A probably damaging Het
Sbno2 T A 10: 79,894,473 (GRCm39) K1067* probably null Het
Sec61g A G 11: 16,456,371 (GRCm39) probably null Het
Slc4a11 A T 2: 130,529,932 (GRCm39) M282K probably benign Het
Slc5a4a T C 10: 76,002,569 (GRCm39) S242P probably benign Het
Sparc A T 11: 55,297,334 (GRCm39) probably null Het
Trrap A T 5: 144,767,761 (GRCm39) T2293S probably benign Het
Ttn T A 2: 76,724,989 (GRCm39) probably benign Het
Vat1l T A 8: 114,998,041 (GRCm39) V195E probably damaging Het
Vmn1r60 T A 7: 5,547,549 (GRCm39) I184F possibly damaging Het
Wdfy4 A G 14: 32,825,940 (GRCm39) I1192T probably damaging Het
Zbtb10 T C 3: 9,345,446 (GRCm39) S737P possibly damaging Het
Zfp553 A G 7: 126,834,517 (GRCm39) E24G probably benign Het
Zscan30 A G 18: 24,104,524 (GRCm39) noncoding transcript 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
R1839:Thra UTSW 11 98,646,969 (GRCm39) missense probably benign 0.01
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'- CCTCCTCAAAGGCCAGAATAGG -3'

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