Mutagenetix > Incidental Mutation

Incidental Mutation 'R5790:Thra'

448293

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

043384-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.903) question?

Stock #

R5790 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

98631539-98659832 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 98653777 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 203 (S203T)

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
AA Change: S203T

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000068281
Gene: ENSMUSG00000058756
AA Change: S203T

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: S203T

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000099428
Gene: ENSMUSG00000058756
AA Change: S203T

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: S203T

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000115323
Gene: ENSMUSG00000058756
AA Change: S203T

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

0.0755

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

99% (73/74)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agbl5	A	T	5: 31,051,702 (GRCm39)	R633*	probably null	Het
Ahnak	T	C	19: 8,992,612 (GRCm39)	V4632A	probably damaging	Het
Asap1	T	A	15: 63,966,114 (GRCm39)	D997V	probably damaging	Het
Atad2	T	C	15: 57,989,990 (GRCm39)	Y162C	probably damaging	Het
Atp2b2	G	T	6: 113,736,270 (GRCm39)	S936R	probably damaging	Het
Bcl11a	T	A	11: 24,113,650 (GRCm39)	L331Q	probably damaging	Het
C6	T	A	15: 4,792,968 (GRCm39)	F358I	probably damaging	Het
Capn15	C	T	17: 26,183,521 (GRCm39)	S386N	probably benign	Het
Ccdc66	G	A	14: 27,222,404 (GRCm39)	T113I	possibly damaging	Het
Cd200	G	T	16: 45,217,621 (GRCm39)	H23Q	possibly damaging	Het
Cdh17	A	G	4: 11,814,945 (GRCm39)		probably null	Het
Ces2b	C	T	8: 105,560,568 (GRCm39)	P128S	probably damaging	Het
Ces3b	A	T	8: 105,819,270 (GRCm39)	Q442L	probably damaging	Het
Chil4	T	C	3: 106,109,894 (GRCm39)	H373R	probably benign	Het
Ciapin1	C	A	8: 95,551,811 (GRCm39)		probably benign	Het
Cnot10	A	C	9: 114,454,985 (GRCm39)		probably null	Het
Cpq	A	G	15: 33,250,143 (GRCm39)	K167E	probably damaging	Het
Dennd4b	T	A	3: 90,184,757 (GRCm39)	D1118E	probably damaging	Het
Dnah8	T	A	17: 31,093,978 (GRCm39)	C4691S	probably damaging	Het
Dnajc1	A	G	2: 18,311,898 (GRCm39)		probably benign	Het
Dnhd1	G	A	7: 105,304,981 (GRCm39)	R341H	probably damaging	Het
Dock10	G	T	1: 80,482,887 (GRCm39)	T2145K	probably benign	Het
Eif3b	T	C	5: 140,427,886 (GRCm39)	V736A	probably benign	Het
Eno1	G	T	4: 150,329,710 (GRCm39)	V195L	probably benign	Het
Ewsr1	C	T	11: 5,032,263 (GRCm39)		probably benign	Het
Fbn2	T	C	18: 58,209,768 (GRCm39)	T1038A	probably benign	Het
Gabrb1	T	C	5: 72,293,827 (GRCm39)	I367T	possibly damaging	Het
Gigyf1	C	T	5: 137,522,517 (GRCm39)		probably benign	Het
Glp2r	T	A	11: 67,655,625 (GRCm39)	Y39F	probably damaging	Het
Gm10036	T	A	18: 15,966,243 (GRCm39)	Y131*	probably null	Het
Gm38706	T	C	6: 130,461,961 (GRCm39)		noncoding transcript	Het
Gna15	G	A	10: 81,345,218 (GRCm39)	R216C	probably damaging	Het
Grin3a	A	G	4: 49,792,717 (GRCm39)	F339L	probably damaging	Het
Grk3	T	G	5: 113,114,842 (GRCm39)	K126T	possibly damaging	Het
Hspa1l	T	C	17: 35,196,216 (GRCm39)	V85A	probably benign	Het
Iqsec1	A	T	6: 90,666,862 (GRCm39)	L525*	probably null	Het
Irx3	T	C	8: 92,526,304 (GRCm39)	T467A	probably benign	Het
Itga2	G	A	13: 115,004,742 (GRCm39)	T530I	probably benign	Het
Lonp2	T	C	8: 87,358,118 (GRCm39)	V113A	probably benign	Het
Msx3	C	T	7: 139,628,866 (GRCm39)	R16H	possibly damaging	Het
Nek3	C	A	8: 22,621,313 (GRCm39)	Q405H	probably damaging	Het
Nek3	T	A	8: 22,621,314 (GRCm39)	Q403L	probably damaging	Het
Or2b6	T	C	13: 21,823,046 (GRCm39)	T216A	probably benign	Het
Or6c66	A	G	10: 129,461,757 (GRCm39)	Y58H	probably damaging	Het
P4ha1	A	G	10: 59,190,184 (GRCm39)	N367S	probably benign	Het
Padi6	C	A	4: 140,459,569 (GRCm39)	G429C	probably damaging	Het
Pidd1	T	C	7: 141,021,305 (GRCm39)		probably benign	Het
Plekhg5	T	C	4: 152,198,392 (GRCm39)	V847A	probably benign	Het
Polr3e	A	G	7: 120,527,190 (GRCm39)	D56G	probably damaging	Het
Pomt2	T	G	12: 87,174,152 (GRCm39)	N347T	probably damaging	Het
Ppp1r9a	T	C	6: 5,134,363 (GRCm39)		probably benign	Het
Rbm33	A	T	5: 28,544,296 (GRCm39)	D184V	probably damaging	Het
Rims2	A	T	15: 39,544,441 (GRCm39)	T1431S	probably damaging	Het
Saal1	T	C	7: 46,351,352 (GRCm39)	D208G	probably damaging	Het
Sis	T	C	3: 72,835,507 (GRCm39)	I952V	probably benign	Het
Slc30a1	T	A	1: 191,640,997 (GRCm39)	D214E	probably benign	Het
Slc30a8	T	C	15: 52,197,043 (GRCm39)	V318A	possibly damaging	Het
Smarca2	A	G	19: 26,654,124 (GRCm39)	T770A	probably damaging	Het
Sptbn4	T	A	7: 27,065,853 (GRCm39)	H2031L	probably damaging	Het
Ssbp1	A	G	6: 40,457,804 (GRCm39)	S141G	probably benign	Het
Tgm4	A	G	9: 122,890,808 (GRCm39)	E45G	probably damaging	Het
Tle2	T	C	10: 81,426,149 (GRCm39)	Y763H	probably damaging	Het
Tmem141	T	A	2: 25,511,087 (GRCm39)	I102L	probably benign	Het
Tmem63c	C	T	12: 87,104,410 (GRCm39)	T77I	probably benign	Het
Tspo2	C	A	17: 48,756,047 (GRCm39)		probably null	Het
Ttc19	T	A	11: 62,172,340 (GRCm39)	M1K	probably null	Het
Ucp1	A	G	8: 84,024,520 (GRCm39)	N282D	possibly damaging	Het
Vmn1r33	A	T	6: 66,589,198 (GRCm39)	F119I	probably benign	Het
Vmn2r24	A	T	6: 123,792,499 (GRCm39)	M609L	probably benign	Het
Vwc2l	A	T	1: 70,790,142 (GRCm39)	H146L	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
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'- TTCCCCTAATGTTGAAGCCTTG -3'
(R):5'- AGAAGAATACCCAGTGAGGCTC -3'

Sequencing Primer
(F):5'- CCTTGAGGCAGAGGCAGAGC -3'
(R):5'- AATACCCAGTGAGGCTCTGTGAC -3'

Posted On

2016-12-15