Mutagenetix > Incidental Mutations

Incidental Mutation 'R4782:Thra'

366646

Institutional Source

Beutler Lab

Gene Symbol

Thra

Ensembl Gene

ENSMUSG00000058756

Gene Name

thyroid hormone receptor alpha

Synonyms

TR alpha 1, Thra2, Thra1, Rvr, TR alpha 2, c-erbAalpha, 6430529J03Rik, Erba, Nr1a1, T3Ralpha, T3R[a]

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.953) question?

Stock #

R4782 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

98740638-98769006 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 98756164 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 37 (S37N)

Ref Sequence

ENSEMBL: ENSMUSP00000123056 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000064187] [ENSMUST00000103139] [ENSMUST00000124072] [ENSMUST00000153043]

Predicted Effect

probably benign
Transcript: ENSMUST00000064187
AA Change: S37N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756
AA Change: S37N

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: ENSMUST00000103139
AA Change: S37N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: S37N

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

Predicted Effect

probably benign
Transcript: ENSMUST00000124072
AA Change: S37N

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756
AA Change: S37N

Domain	Start	End	E-Value	Type
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

noncoding transcript
Transcript: ENSMUST00000152195

Predicted Effect

probably benign
Transcript: ENSMUST00000153043
AA Change: S37N

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153468

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

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: 121 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	G	11: 9,328,096	E3092G	probably damaging	Het
Abhd12b	C	G	12: 70,169,064	S170C	probably damaging	Het
Abtb2	A	T	2: 103,717,299	D1006V	probably benign	Het
Adgrl1	A	G	8: 83,935,573	H1021R	probably benign	Het
Ago3	A	T	4: 126,347,872		probably null	Het
Ahnak	A	G	19: 9,012,499		probably benign	Het
Akap6	CA	C	12: 52,887,623		probably null	Het
Amotl2	T	G	9: 102,720,123		probably null	Het
Ankrd34b	T	A	13: 92,438,305	I15N	probably damaging	Het
Ap3d1	C	T	10: 80,721,586		probably null	Het
Appl2	A	T	10: 83,600,991	D635E	probably damaging	Het
Arid1b	C	T	17: 5,339,221	P1681S	probably damaging	Het
Atp10a	T	C	7: 58,791,095	M496T	probably benign	Het
Atp2c2	A	G	8: 119,749,152	K595E	probably damaging	Het
Atpaf2	T	C	11: 60,404,412	H204R	probably damaging	Het
Atr	G	A	9: 95,862,797	V56I	probably benign	Het
Bod1l	G	A	5: 41,833,663	T183I	probably benign	Het
Btbd11	A	C	10: 85,654,550	I1027L	probably damaging	Het
Ccdc171	A	T	4: 83,681,016	E689D	probably damaging	Het
Cdc73	T	A	1: 143,627,875	Q346L	probably benign	Het
Chd2	A	T	7: 73,484,436	M721K	possibly damaging	Het
Col22a1	T	A	15: 71,801,925	T981S	unknown	Het
Col4a3bp	T	C	13: 96,612,265	V281A	probably benign	Het
Cpox	G	A	16: 58,672,623	A207T	probably damaging	Het
Cym	G	A	3: 107,216,097	T160I	possibly damaging	Het
D130043K22Rik	T	C	13: 24,878,040	I664T	probably damaging	Het
Ddx4	C	T	13: 112,613,696		probably null	Het
Ddx4	A	T	13: 112,651,360	V15E	probably benign	Het
Depdc1a	G	A	3: 159,526,636	E675K	probably damaging	Het
Dglucy	A	T	12: 100,850,343	M415L	probably benign	Het
Dlg4	C	T	11: 70,026,954	P21L	probably damaging	Het
Dmxl1	A	T	18: 49,862,992	N395I	probably damaging	Het
Dzank1	A	T	2: 144,504,399	C249S	probably damaging	Het
Efnb2	A	T	8: 8,623,104		probably null	Het
Ercc6l2	T	G	13: 63,834,738	I244S	probably damaging	Het
Ewsr1	A	T	11: 5,070,423	M584K	unknown	Het
Fam193b	A	G	13: 55,543,471	S197P	probably damaging	Het
Fanca	A	G	8: 123,288,202	V689A	probably damaging	Het
Fbxo31	A	T	8: 121,552,439	Y436*	probably null	Het
Fbxo31	A	G	8: 121,552,441	Y436H	probably damaging	Het
Fcna	T	A	2: 25,625,326	D215V	probably damaging	Het
Foxj3	A	T	4: 119,621,660	S438C	unknown	Het
Gcm2	T	C	13: 41,103,494	K260E	possibly damaging	Het
Gcnt4	A	T	13: 96,947,406	L403F	possibly damaging	Het
Gdf10	A	G	14: 33,931,913	T126A	probably benign	Het
Ggcx	A	G	6: 72,428,892	K569E	probably benign	Het
Gm10250	C	T	15: 5,121,096		probably benign	Het
Gm8251	T	C	1: 44,059,043	D965G	possibly damaging	Het
Gpnmb	G	T	6: 49,045,483		probably null	Het
Ifi44	G	A	3: 151,745,592	P241S	probably damaging	Het
Irs1	T	C	1: 82,287,463	T1011A	probably benign	Het
Jag2	A	T	12: 112,914,249	S595T	probably benign	Het
Kif5a	T	A	10: 127,230,954	Q960L	probably benign	Het
Kifc2	A	G	15: 76,664,348	E430G	possibly damaging	Het
Lama3	T	A	18: 12,411,570	C323*	probably null	Het
Lgsn	T	C	1: 31,203,742	Y302H	probably benign	Het
Lmbrd1	G	A	1: 24,744,975		probably null	Het
Lrpap1	A	G	5: 35,099,278	V120A	probably damaging	Het
Macrod2	T	A	2: 140,419,938	D46E	possibly damaging	Het
Mbd4	C	A	6: 115,845,322	R63L	possibly damaging	Het
Mfsd10	T	C	5: 34,634,949		probably benign	Het
Mib2	G	T	4: 155,659,772	S144R	probably benign	Het
Muc5b	T	A	7: 141,847,716	C566*	probably null	Het
Ndufs1	C	A	1: 63,160,949	G268V	probably damaging	Het
Nfs1	A	G	2: 156,134,449	V175A	possibly damaging	Het
Ngb	G	A	12: 87,100,225	H73Y	probably benign	Het
Npepps	G	A	11: 97,226,826	T549I	probably damaging	Het
Nr1h2	A	G	7: 44,550,499	V329A	possibly damaging	Het
Nsun6	T	C	2: 15,036,326	I151M	possibly damaging	Het
Ofcc1	T	C	13: 40,001,892		probably null	Het
Olfr1388	T	A	11: 49,443,869	F6Y	probably benign	Het
Olfr262	C	T	19: 12,241,572	V30I	probably benign	Het
Olfr372	A	G	8: 72,058,094	N138S	probably benign	Het
Olfr391-ps	C	T	11: 73,798,839	C306Y	probably benign	Het
Olfr555	T	A	7: 102,658,834	N4K	possibly damaging	Het
Olfr910	A	G	9: 38,539,075	Y60C	probably damaging	Het
Parp6	A	G	9: 59,634,984		probably null	Het
Pcnt	C	A	10: 76,409,577	R1075S	possibly damaging	Het
Pla2g4f	T	C	2: 120,303,276	E548G	probably damaging	Het
Polrmt	G	T	10: 79,739,523	H725N	probably benign	Het
Pou2f3	T	C	9: 43,139,858	T178A	probably damaging	Het
Prtn3	C	A	10: 79,882,065	P169H	probably damaging	Het
Ptprd	A	G	4: 76,091,532	I764T	probably benign	Het
Ptprh	A	T	7: 4,569,577	H467Q	probably benign	Het
Raph1	A	T	1: 60,489,114	I996N	probably damaging	Het
Rasa4	G	A	5: 136,091,229	W53*	probably null	Het
Rasgrp1	C	T	2: 117,284,875	R744Q	probably benign	Het
Rmnd5a	T	C	6: 71,413,349	E141G	probably damaging	Het
Rps12	T	C	10: 23,786,790	I51M	possibly damaging	Het
Scn10a	T	G	9: 119,622,910	S1316R	possibly damaging	Het
Sdhb	A	G	4: 140,977,466	H246R	possibly damaging	Het
Setx	G	A	2: 29,144,046	R332Q	probably damaging	Het
Siglec1	A	C	2: 131,075,923	S1011R	probably damaging	Het
Sin3b	A	C	8: 72,725,643	I126L	probably benign	Het
Slc11a1	T	G	1: 74,384,088	L366R	probably damaging	Het
Slc12a1	C	T	2: 125,161,079	R177*	probably null	Het
Slc30a1	A	C	1: 191,909,048	K269Q	probably benign	Het
Slco1a5	T	C	6: 142,248,807	Y370C	possibly damaging	Het
Slf2	T	A	19: 44,934,925		probably null	Het
Sltm	A	G	9: 70,589,057	H958R	probably damaging	Het
Snrnp40	A	G	4: 130,362,756	I91M	probably damaging	Het
Spta1	A	T	1: 174,230,666	Q1900L	probably benign	Het
Srgn	C	T	10: 62,497,852	E49K	possibly damaging	Het
Ssu2	A	C	6: 112,376,450	C238G	probably damaging	Het
Terf2	G	T	8: 107,076,675	H425Q	probably benign	Het
Toporsl	A	G	4: 52,610,845	D246G	probably damaging	Het
Ubap2l	G	A	3: 90,020,903	T553M	probably damaging	Het
Usp10	A	G	8: 119,941,191	Y77C	probably benign	Het
Utrn	T	C	10: 12,750,069	T123A	probably damaging	Het
Vmn1r204	T	G	13: 22,556,697	F166C	probably benign	Het
Vmn2r14	T	C	5: 109,221,504	I68V	probably benign	Het
Wls	C	T	3: 159,897,445	T165I	probably benign	Het
Wsb1	A	G	11: 79,240,373	M399T	probably benign	Het
Xbp1	C	T	11: 5,521,167	T58M	probably damaging	Het
Zbtb46	A	T	2: 181,391,136	D577E	probably benign	Het
Zfp366	A	G	13: 99,246,483	D718G	probably damaging	Het
Zfp408	A	T	2: 91,645,024	V595E	possibly damaging	Het
Zfp493	T	A	13: 67,786,203	W60R	probably null	Het
Zfp606	A	T	7: 12,494,005	K626N	probably damaging	Het
Zfp820	A	T	17: 21,818,985	L454Q	probably benign	Het
Zswim5	A	G	4: 116,972,972	I515V	probably benign	Het

Other mutations in Thra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01021:Thra	APN	11	98762928	missense	possibly damaging	0.90
IGL01544:Thra	APN	11	98756928	missense	possibly damaging	0.46
IGL02377:Thra	APN	11	98761916	missense	probably damaging	1.00
IGL02738:Thra	APN	11	98764359	missense	probably benign	0.40
IGL03111:Thra	APN	11	98761029	unclassified	probably benign
R0033:Thra	UTSW	11	98764352	missense	probably benign	0.00
R0033:Thra	UTSW	11	98764352	missense	probably benign	0.00
R0959:Thra	UTSW	11	98753629	missense	possibly damaging	0.94
R1659:Thra	UTSW	11	98756979	missense	probably damaging	0.99
R1839:Thra	UTSW	11	98756143	missense	probably benign	0.01
R1859:Thra	UTSW	11	98756151	missense	probably damaging	0.98
R1935:Thra	UTSW	11	98763073	splice site	probably benign
R1956:Thra	UTSW	11	98763741	missense	probably benign	0.03
R4584:Thra	UTSW	11	98764484	missense	probably benign	0.42
R5414:Thra	UTSW	11	98760957	missense	probably benign	0.34
R5790:Thra	UTSW	11	98762951	missense	probably benign	0.20
R5927:Thra	UTSW	11	98763688	missense	possibly damaging	0.56

Predicted Primers

PCR Primer
(F):5'- GACCCTTTCCAAGCTTTGTCAG -3'
(R):5'- CCTCCTCAAAGGCCAGAATAGG -3'

Sequencing Primer
(F):5'- GCTTTGTCAGCTGATATAGGGG -3'
(R):5'- CTCCTCAAAGGCCAGAATAGGTTTTG -3'

Posted On

2015-12-29