Mutagenetix > Incidental Mutation

Incidental Mutation 'R4584:Thra'

343943

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

041805-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.903) question?

Stock #

R4584 (G1)

Quality Score

212

Status

Validated

Chromosome

Chromosomal Location

98631539-98659832 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 98655310 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 397 (F397L)

Ref Sequence

ENSEMBL: ENSMUSP00000099428 (fasta)

Gene Model

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

AlphaFold

P63058

Predicted Effect

probably benign
Transcript: ENSMUST00000064187

SMART Domains

Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756

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

probably benign
Transcript: ENSMUST00000103139
AA Change: F397L

PolyPhen 2 Score 0.424 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: F397L

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

SMART Domains

Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756

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: ENSMUST00000139220

Meta Mutation Damage Score

0.0864

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

97% (86/89)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6430548M08Rik	A	G	8: 120,886,756 (GRCm39)	N343D	probably damaging	Het
9530002B09Rik	T	A	4: 122,594,979 (GRCm39)	D78E	possibly damaging	Het
A2m	C	A	6: 121,634,365 (GRCm39)	D632E	probably benign	Het
Alpk2	A	G	18: 65,440,035 (GRCm39)	S453P	probably damaging	Het
Birc2	A	T	9: 7,833,675 (GRCm39)	F269I	probably damaging	Het
Ccdc66	G	A	14: 27,222,468 (GRCm39)	P92S	probably benign	Het
Cdc34	T	A	10: 79,523,869 (GRCm39)	D108E	possibly damaging	Het
Cdk5rap2	A	C	4: 70,184,997 (GRCm39)	V1151G	probably damaging	Het
Cemip	T	C	7: 83,607,747 (GRCm39)	K753R	probably damaging	Het
Cep295	A	T	9: 15,246,095 (GRCm39)	L787Q	possibly damaging	Het
Cideb	T	C	14: 55,995,727 (GRCm39)	N8S	probably benign	Het
Dagla	A	G	19: 10,248,373 (GRCm39)	Y96H	probably damaging	Het
Dapl1	C	A	2: 59,335,086 (GRCm39)	T80K	possibly damaging	Het
Ddx6	T	C	9: 44,535,784 (GRCm39)	V171A	probably damaging	Het
Dnah12	C	A	14: 26,494,551 (GRCm39)	T34K	probably damaging	Het
Dnhd1	T	C	7: 105,327,256 (GRCm39)	L735P	probably damaging	Het
Ep400	T	A	5: 110,881,763 (GRCm39)		probably benign	Het
Erlin1	G	T	19: 44,057,758 (GRCm39)	Y22*	probably null	Het
Gmcl1	A	G	6: 86,699,605 (GRCm39)	S141P	probably damaging	Het
Gtf2a1	C	T	12: 91,529,700 (GRCm39)	V338I	possibly damaging	Het
H2-T15	A	T	17: 36,368,559 (GRCm39)	M123K	probably damaging	Het
Ighv1-66	T	A	12: 115,557,016 (GRCm39)	Q22L	possibly damaging	Het
Igkv4-80	T	C	6: 68,993,720 (GRCm39)	Y57C	probably damaging	Het
Itpk1	G	A	12: 102,536,416 (GRCm39)	A410V	possibly damaging	Het
Itsn1	T	A	16: 91,617,471 (GRCm39)		probably benign	Het
Kcnk3	G	T	5: 30,745,730 (GRCm39)	A24S	probably damaging	Het
Kif20a	A	G	18: 34,765,664 (GRCm39)	Y887C	probably damaging	Het
Klf13	T	C	7: 63,587,718 (GRCm39)	T193A	possibly damaging	Het
Klhl9	G	T	4: 88,640,144 (GRCm39)	H32Q	probably damaging	Het
Kndc1	C	G	7: 139,481,159 (GRCm39)	P82A	probably damaging	Het
Llgl1	T	A	11: 60,602,908 (GRCm39)	L861Q	probably damaging	Het
Lpcat2	A	G	8: 93,615,999 (GRCm39)	E305G	probably damaging	Het
Mib2	C	A	4: 155,741,744 (GRCm39)	A293S	probably damaging	Het
Mtfr1	A	G	3: 19,269,766 (GRCm39)	E138G	probably damaging	Het
Myoz1	A	G	14: 20,700,663 (GRCm39)	W185R	probably damaging	Het
Ninj1	T	A	13: 49,347,442 (GRCm39)		probably null	Het
Nlgn2	A	T	11: 69,725,104 (GRCm39)	V54E	possibly damaging	Het
Nlrc5	A	C	8: 95,203,903 (GRCm39)	I668L	probably damaging	Het
Npy6r	T	A	18: 44,409,262 (GRCm39)	C228S	probably damaging	Het
Nufip2	T	C	11: 77,632,554 (GRCm39)	V690A	unknown	Het
Nup107	T	C	10: 117,602,273 (GRCm39)	I513M	probably benign	Het
Oit3	T	C	10: 59,261,284 (GRCm39)	D461G	probably damaging	Het
Or2ab1	T	A	11: 58,488,830 (GRCm39)	F205I	probably benign	Het
Paxbp1	T	C	16: 90,831,011 (GRCm39)	D455G	probably damaging	Het
Pcdh7	A	T	5: 57,878,625 (GRCm39)	T727S	probably damaging	Het
Pex14	G	A	4: 149,055,053 (GRCm39)	A113V	probably damaging	Het
Phc3	A	G	3: 31,020,031 (GRCm39)	V23A	possibly damaging	Het
Plec	T	C	15: 76,115,406 (GRCm39)	D56G	possibly damaging	Het
Plekha7	C	A	7: 115,836,768 (GRCm39)		probably benign	Het
Prdm16	T	C	4: 154,422,140 (GRCm39)	E885G	probably damaging	Het
Prss1l	T	C	6: 41,373,701 (GRCm39)	L188P	probably benign	Het
Psd2	A	G	18: 36,145,881 (GRCm39)	T762A	probably benign	Het
Psme4	T	A	11: 30,784,318 (GRCm39)	H964Q	probably damaging	Het
Rbak	C	T	5: 143,161,878 (GRCm39)	V51I	probably benign	Het
Rbfa	A	G	18: 80,243,721 (GRCm39)	L15P	probably benign	Het
Ren1	T	C	1: 133,282,546 (GRCm39)	Y84H	probably damaging	Het
Rps6ka5	A	T	12: 100,547,577 (GRCm39)	I311N	probably damaging	Het
Samd14	T	A	11: 94,912,361 (GRCm39)		probably null	Het
Scaf4	T	C	16: 90,026,403 (GRCm39)		probably benign	Het
Serpina12	A	T	12: 104,004,611 (GRCm39)	L7Q	unknown	Het
Serpinb9d	A	T	13: 33,384,599 (GRCm39)	E192V	probably damaging	Het
Slc22a29	A	T	19: 8,146,655 (GRCm39)	F382L	probably benign	Het
Snta1	T	A	2: 154,220,035 (GRCm39)	D375V	probably benign	Het
Stat5b	T	A	11: 100,678,064 (GRCm39)	Y683F	probably damaging	Het
Strip1	A	T	3: 107,531,819 (GRCm39)	Y257N	probably benign	Het
Sugp2	A	G	8: 70,704,548 (GRCm39)	H695R	probably benign	Het
Svep1	T	A	4: 58,068,526 (GRCm39)	R3087*	probably null	Het
Syngr2	T	C	11: 117,703,947 (GRCm39)	V138A	probably damaging	Het
Tmem45b	T	A	9: 31,339,951 (GRCm39)	I149F	probably damaging	Het
Tmprss11f	C	T	5: 86,687,553 (GRCm39)		probably null	Het
Ush2a	C	T	1: 188,183,995 (GRCm39)	T1433I	probably benign	Het
Vmn2r109	A	T	17: 20,774,820 (GRCm39)	Y178*	probably null	Het
Vmn2r84	T	G	10: 130,226,582 (GRCm39)	M419L	probably benign	Het
Wnk2	C	T	13: 49,244,313 (GRCm39)	D508N	probably damaging	Het
Zfp268	T	A	4: 145,343,747 (GRCm39)		probably null	Het
Zfp276	A	G	8: 123,995,145 (GRCm39)		probably benign	Het
Zfp568	T	G	7: 29,697,617 (GRCm39)	F100V	probably benign	Het
Zfp667	T	A	7: 6,293,624 (GRCm39)	D41E	possibly 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
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'- TGCTGTGCGTGGACAAGATC -3'
(R):5'- TCATTTATGGCCCTGTCCAAG -3'

Sequencing Primer
(F):5'- TCGAGAAGAGTCAGGAGGCCTAC -3'
(R):5'- GGTGTATGGGAGCTGCATCTATCC -3'

Posted On

2015-09-24