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

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

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.891) question?

Stock #

R7307 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

98740638-98769006 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 98764308 bp (GRCm38)

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: 17,118,395	P155L	probably benign	Het
Adamts12	G	T	15: 11,217,813	L285F	probably damaging	Het
Ankrd6	A	T	4: 32,816,949	Y393N	possibly damaging	Het
Arhgap45	A	G	10: 80,029,182	Q993R	probably benign	Het
Arhgef33	G	C	17: 80,347,120		probably null	Het
B4galnt3	T	C	6: 120,215,431	D448G	probably benign	Het
Capn1	C	G	19: 5,993,908	E564D	possibly damaging	Het
Ccdc85a	A	G	11: 28,399,384	S474P	probably benign	Het
Cdk12	T	A	11: 98,249,800	L1289*	probably null	Het
Cramp1l	A	T	17: 24,974,745	N920K	possibly damaging	Het
Cubn	C	T	2: 13,340,332	S2091N	probably damaging	Het
Ddx1	A	T	12: 13,223,959	I581N	probably damaging	Het
Dnm2	A	T	9: 21,485,687	N487Y	probably damaging	Het
Enc1	A	C	13: 97,245,093	N37T	probably damaging	Het
Ephb3	T	G	16: 21,222,226	I932S	probably benign	Het
Frk	T	A	10: 34,591,938	M316K	probably damaging	Het
Gdap2	C	T	3: 100,202,033	R25C	unknown	Het
Gm10436	A	C	12: 88,181,749	C32W	probably damaging	Het
Gpat2	T	A	2: 127,434,890	D671E	probably damaging	Het
Gpr179	C	T	11: 97,338,846	E828K	probably benign	Het
Greb1l	T	C	18: 10,538,142	Y1052H	probably damaging	Het
Gtf2f1	C	T	17: 57,007,833	S69N	probably damaging	Het
Hid1	A	C	11: 115,348,482	I785S	probably damaging	Het
Hmcn2	T	C	2: 31,343,081	I214T	probably damaging	Het
Hsd3b5	G	T	3: 98,619,769	F120L	probably damaging	Het
Kif16b	C	T	2: 142,712,931	R649Q	probably benign	Het
Kif17	A	T	4: 138,262,643	E47D	probably benign	Het
Kmt2b	T	C	7: 30,580,471	H1368R	probably damaging	Het
Kmt2d	A	T	15: 98,849,418	S3342T	unknown	Het
Krt82	A	G	15: 101,542,907	C356R	probably damaging	Het
Lrit2	A	G	14: 37,072,199	K407E	probably benign	Het
Malt1	T	A	18: 65,451,569	H325Q	possibly damaging	Het
Mccc2	T	G	13: 99,988,600	D187A	possibly damaging	Het
Mgll	T	A	6: 88,814,121		probably null	Het
Mindy2	T	G	9: 70,610,959	E449A	possibly damaging	Het
Muc5b	G	A	7: 141,842,294	V96M	unknown	Het
Nlrp4e	A	G	7: 23,321,528	E480G	probably benign	Het
Nup98	A	G	7: 102,134,795	I1093T	probably benign	Het
Olfr1288	A	T	2: 111,478,760		probably benign	Het
Olfr243	G	T	7: 103,716,966	R124L	probably damaging	Het
Olfr350	G	A	2: 36,850,125	M26I	probably benign	Het
Olfr541	G	A	7: 140,705,147	V299I	probably benign	Het
Pcdhb6	A	T	18: 37,335,478	H484L	probably benign	Het
Phldb1	T	C	9: 44,694,047	T604A	possibly damaging	Het
Pitpnm3	G	T	11: 72,070,964	A275D	probably damaging	Het
Polr2a	A	T	11: 69,747,292		probably null	Het
Polr3a	A	G	14: 24,459,987	C960R	probably benign	Het
Pou6f2	G	A	13: 18,239,713	A159V		Het
Pramef6	A	C	4: 143,896,775	Y276*	probably null	Het
Psmc4	A	G	7: 28,042,660	V303A	probably benign	Het
Ptdss2	A	G	7: 141,151,732	N151S	possibly damaging	Het
Ptprk	T	A	10: 28,589,008	Y1295*	probably null	Het
Rbm19	A	G	5: 120,186,218	K881E	possibly damaging	Het
Rcan2	T	A	17: 44,021,102	Y183*	probably null	Het
Rnd1	T	C	15: 98,670,799	E166G	probably damaging	Het
Rnf113a2	T	A	12: 84,418,179	C282S	probably damaging	Het
S100b	G	A	10: 76,257,092	G20R	probably benign	Het
Sae1	G	T	7: 16,368,544	Y168*	probably null	Het
Samd9l	C	A	6: 3,372,600	G1554*	probably null	Het
Samhd1	T	C	2: 157,135,020	S55G	probably benign	Het
Sgsm1	T	C	5: 113,273,646	D525G	probably benign	Het
Slc28a3	A	T	13: 58,563,172	M512K	probably damaging	Het
Slc9b2	T	A	3: 135,318,390	N67K	probably benign	Het
Smarca4	T	A	9: 21,638,800	I402N	probably damaging	Het
St7l	T	C	3: 104,889,353	F261L	probably benign	Het
Syde2	T	A	3: 146,015,798	V1140D	probably damaging	Het
Syt6	T	A	3: 103,587,472	I251N	probably damaging	Het
Taok2	T	C	7: 126,866,818	E916G	probably damaging	Het
Tecta	A	G	9: 42,377,992	S426P	probably damaging	Het
Trub1	A	T	19: 57,472,703	Y137F	probably damaging	Het
Vps13b	T	C	15: 35,841,545	F2574L	probably benign	Het
Ythdf3	T	C	3: 16,183,500	S2P	possibly damaging	Het
Zc3h13	T	A	14: 75,330,541	D1091E	probably damaging	Het
Zdhhc6	A	G	19: 55,313,250	Y100H	probably damaging	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
California	UTSW	11	98764308	missense	probably damaging	0.97
Crissal	UTSW	11	98762951	missense	probably benign	0.20
R0033_Thra_272	UTSW	11	98764352	missense	probably benign	0.00
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
R4782:Thra	UTSW	11	98756164	missense	probably benign	0.01
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
R7207:Thra	UTSW	11	98760976	missense	probably damaging	1.00
R7234:Thra	UTSW	11	98763718	missense	probably damaging	1.00
R7825:Thra	UTSW	11	98762948	missense	probably benign	0.14
R7875:Thra	UTSW	11	98768431	missense	probably damaging	0.98
R8385:Thra	UTSW	11	98768351	missense	probably benign	0.40
R8669:Thra	UTSW	11	98763650	missense	possibly damaging	0.89
R8955:Thra	UTSW	11	98753623	missense	possibly damaging	0.92
R9549:Thra	UTSW	11	98762946	missense	probably benign	0.14
R9615:Thra	UTSW	11	98760889	missense	probably damaging	1.00
Z1177:Thra	UTSW	11	98753481	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