Mutagenetix > Incidental Mutation

Incidental Mutation 'R7307:Thra'

567330

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

045366-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.914) question?

Stock #

R7307 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

98631539-98659832 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 98655134 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 338 (I338T)

Ref Sequence

ENSEMBL: ENSMUSP00000068281 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000064187] [ENSMUST00000064941] [ENSMUST00000103139] [ENSMUST00000124072]

AlphaFold

P63058

Predicted Effect

probably damaging
Transcript: ENSMUST00000064187
AA Change: I338T

PolyPhen 2 Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756
AA Change: I338T

Domain	Start	End	E-Value	Type
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: ENSMUST00000064941

SMART Domains

Protein: ENSMUSP00000069505
Gene: ENSMUSG00000020889

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
low complexity region	70	94	N/A	INTRINSIC
ZnF_C4	130	202	5.54e-38	SMART
low complexity region	240	263	N/A	INTRINSIC
PDB:3N00\|A	282	361	2e-21	PDB
HOLI	442	600	4.2e-38	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000103139
AA Change: I338T

PolyPhen 2 Score 0.543 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: I338T

Domain	Start	End	E-Value	Type
ZnF_C4	50	123	3.09e-36	SMART
HOLI	220	378	7.26e-33	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000124072
AA Change: I338T

PolyPhen 2 Score 0.839 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756
AA Change: I338T

Domain	Start	End	E-Value	Type
ZnF_C4	50	123	3.09e-36	SMART
HOLI	220	378	2.36e-32	SMART

Meta Mutation Damage Score

0.9508

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (75/75)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610318N02Rik	G	A	16: 16,936,259 (GRCm39)	P155L	probably benign	Het
Adamts12	G	T	15: 11,217,899 (GRCm39)	L285F	probably damaging	Het
Ankrd6	A	T	4: 32,816,949 (GRCm39)	Y393N	possibly damaging	Het
Arhgap45	A	G	10: 79,865,016 (GRCm39)	Q993R	probably benign	Het
Arhgef33	G	C	17: 80,654,549 (GRCm39)		probably null	Het
B4galnt3	T	C	6: 120,192,392 (GRCm39)	D448G	probably benign	Het
Capn1	C	G	19: 6,043,938 (GRCm39)	E564D	possibly damaging	Het
Ccdc85a	A	G	11: 28,349,384 (GRCm39)	S474P	probably benign	Het
Cdk12	T	A	11: 98,140,626 (GRCm39)	L1289*	probably null	Het
Cramp1	A	T	17: 25,193,719 (GRCm39)	N920K	possibly damaging	Het
Cubn	C	T	2: 13,345,143 (GRCm39)	S2091N	probably damaging	Het
Ddx1	A	T	12: 13,273,960 (GRCm39)	I581N	probably damaging	Het
Dnm2	A	T	9: 21,396,983 (GRCm39)	N487Y	probably damaging	Het
Enc1	A	C	13: 97,381,601 (GRCm39)	N37T	probably damaging	Het
Ephb3	T	G	16: 21,040,976 (GRCm39)	I932S	probably benign	Het
Frk	T	A	10: 34,467,934 (GRCm39)	M316K	probably damaging	Het
Gdap2	C	T	3: 100,109,349 (GRCm39)	R25C	unknown	Het
Gpat2	T	A	2: 127,276,810 (GRCm39)	D671E	probably damaging	Het
Gpr179	C	T	11: 97,229,672 (GRCm39)	E828K	probably benign	Het
Greb1l	T	C	18: 10,538,142 (GRCm39)	Y1052H	probably damaging	Het
Gtf2f1	C	T	17: 57,314,833 (GRCm39)	S69N	probably damaging	Het
Hid1	A	C	11: 115,239,308 (GRCm39)	I785S	probably damaging	Het
Hmcn2	T	C	2: 31,233,093 (GRCm39)	I214T	probably damaging	Het
Hsd3b5	G	T	3: 98,527,085 (GRCm39)	F120L	probably damaging	Het
Kif16b	C	T	2: 142,554,851 (GRCm39)	R649Q	probably benign	Het
Kif17	A	T	4: 137,989,954 (GRCm39)	E47D	probably benign	Het
Kmt2b	T	C	7: 30,279,896 (GRCm39)	H1368R	probably damaging	Het
Kmt2d	A	T	15: 98,747,299 (GRCm39)	S3342T	unknown	Het
Krt82	A	G	15: 101,451,342 (GRCm39)	C356R	probably damaging	Het
Lrit2	A	G	14: 36,794,156 (GRCm39)	K407E	probably benign	Het
Malt1	T	A	18: 65,584,640 (GRCm39)	H325Q	possibly damaging	Het
Mccc2	T	G	13: 100,125,108 (GRCm39)	D187A	possibly damaging	Het
Mgll	T	A	6: 88,791,103 (GRCm39)		probably null	Het
Mindy2	T	G	9: 70,518,241 (GRCm39)	E449A	possibly damaging	Het
Muc5b	G	A	7: 141,396,031 (GRCm39)	V96M	unknown	Het
Nlrp4e	A	G	7: 23,020,953 (GRCm39)	E480G	probably benign	Het
Nup98	A	G	7: 101,784,002 (GRCm39)	I1093T	probably benign	Het
Or13a26	G	A	7: 140,285,060 (GRCm39)	V299I	probably benign	Het
Or1j4	G	A	2: 36,740,137 (GRCm39)	M26I	probably benign	Het
Or4g7	A	T	2: 111,309,105 (GRCm39)		probably benign	Het
Or52a20	G	T	7: 103,366,173 (GRCm39)	R124L	probably damaging	Het
Pcdhb6	A	T	18: 37,468,531 (GRCm39)	H484L	probably benign	Het
Phldb1	T	C	9: 44,605,344 (GRCm39)	T604A	possibly damaging	Het
Pitpnm3	G	T	11: 71,961,790 (GRCm39)	A275D	probably damaging	Het
Polr2a	A	T	11: 69,638,118 (GRCm39)		probably null	Het
Polr3a	A	G	14: 24,510,055 (GRCm39)	C960R	probably benign	Het
Pou6f2	G	A	13: 18,414,298 (GRCm39)	A159V		Het
Pramel11	A	C	4: 143,623,345 (GRCm39)	Y276*	probably null	Het
Pramel51	A	C	12: 88,148,519 (GRCm39)	C32W	probably damaging	Het
Psmc4	A	G	7: 27,742,085 (GRCm39)	V303A	probably benign	Het
Ptdss2	A	G	7: 140,731,645 (GRCm39)	N151S	possibly damaging	Het
Ptprk	T	A	10: 28,465,004 (GRCm39)	Y1295*	probably null	Het
Rbm19	A	G	5: 120,324,283 (GRCm39)	K881E	possibly damaging	Het
Rcan2	T	A	17: 44,331,993 (GRCm39)	Y183*	probably null	Het
Rnd1	T	C	15: 98,568,680 (GRCm39)	E166G	probably damaging	Het
Rnf113a2	T	A	12: 84,464,953 (GRCm39)	C282S	probably damaging	Het
S100b	G	A	10: 76,092,926 (GRCm39)	G20R	probably benign	Het
Sae1	G	T	7: 16,102,469 (GRCm39)	Y168*	probably null	Het
Samd9l	C	A	6: 3,372,600 (GRCm39)	G1554*	probably null	Het
Samhd1	T	C	2: 156,976,940 (GRCm39)	S55G	probably benign	Het
Sgsm1	T	C	5: 113,421,512 (GRCm39)	D525G	probably benign	Het
Slc28a3	A	T	13: 58,710,986 (GRCm39)	M512K	probably damaging	Het
Slc9b2	T	A	3: 135,024,151 (GRCm39)	N67K	probably benign	Het
Smarca4	T	A	9: 21,550,096 (GRCm39)	I402N	probably damaging	Het
St7l	T	C	3: 104,796,669 (GRCm39)	F261L	probably benign	Het
Syde2	T	A	3: 145,721,553 (GRCm39)	V1140D	probably damaging	Het
Syt6	T	A	3: 103,494,788 (GRCm39)	I251N	probably damaging	Het
Taok2	T	C	7: 126,465,990 (GRCm39)	E916G	probably damaging	Het
Tecta	A	G	9: 42,289,288 (GRCm39)	S426P	probably damaging	Het
Trub1	A	T	19: 57,461,135 (GRCm39)	Y137F	probably damaging	Het
Vps13b	T	C	15: 35,841,691 (GRCm39)	F2574L	probably benign	Het
Ythdf3	T	C	3: 16,237,664 (GRCm39)	S2P	possibly damaging	Het
Zc3h13	T	A	14: 75,567,981 (GRCm39)	D1091E	probably damaging	Het
Zdhhc6	A	G	19: 55,301,682 (GRCm39)	Y100H	probably damaging	Het

Other mutations in Thra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- TTATGGATTGCTTCATGGCCGC -3'
(R):5'- TGGGGCACTCGACTTTCATG -3'

Sequencing Primer
(F):5'- AGTGTCCCTCCCTGAGC -3'
(R):5'- CACTCGACTTTCATGTGGAGGAAG -3'

Posted On

2019-06-26