Mutagenetix > Incidental Mutation

Incidental Mutation 'R5288:Tbp'

424549

Institutional Source

Beutler Lab

Gene Symbol

Tbp

Ensembl Gene

ENSMUSG00000014767

Gene Name

TATA box binding protein

Synonyms

Gtf2d

MMRRC Submission

042842-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5288 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

15720150-15737689 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 15727609 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 145 (I145V)

Ref Sequence

ENSEMBL: ENSMUSP00000120484 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000014911] [ENSMUST00000117593] [ENSMUST00000118001] [ENSMUST00000119879] [ENSMUST00000143924] [ENSMUST00000147081] [ENSMUST00000153480] [ENSMUST00000162505] [ENSMUST00000159197] [ENSMUST00000155051]

AlphaFold

P29037

Predicted Effect

probably benign
Transcript: ENSMUST00000014911
AA Change: I145V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000014911
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	138	222	4.3e-34	PFAM
Pfam:TBP	227	313	3.4e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117593
AA Change: I145V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000112794
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	138	222	4.3e-34	PFAM
Pfam:TBP	227	313	3.4e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118001
AA Change: I145V

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000113999
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	138	204	1.4e-29	PFAM
Pfam:TBP	203	257	4.4e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119879
AA Change: I145V

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000114007
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	138	222	8.9e-35	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000143924
AA Change: I145V

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000122696
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000147081
AA Change: I145V

PolyPhen 2 Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000120484
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	138	178	9.6e-12	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153480

SMART Domains

Protein: ENSMUSP00000114471
Gene: ENSMUSG00000014767

Domain	Start	End	E-Value	Type
Pfam:TBP	30	114	5e-35	PFAM
Pfam:TBP	119	205	4.4e-37	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162505
AA Change: I145V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000124317
Gene: ENSMUSG00000014767
AA Change: I145V

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	139	221	1.1e-34	PFAM
Pfam:TBP	229	312	8.5e-34	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000159197

SMART Domains

Protein: ENSMUSP00000125691
Gene: ENSMUSG00000014767

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	128	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000155051

SMART Domains

Protein: ENSMUSP00000117551
Gene: ENSMUSG00000014767

Domain	Start	End	E-Value	Type
low complexity region	55	70	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232661

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes TBP, the TATA-binding protein. A distinctive feature of TBP is a long string of glutamines in the N-terminus. This region of the protein modulates the DNA binding activity of the C terminus, and modulation of DNA binding affects the rate of transcription complex formation and initiation of transcription. The number of CAG repeats encoding the polyglutamine tract is usually 25-42, and expansion of the number of repeats to 45-66 increases the length of the polyglutamine string and is associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for one null allele exhibit embryonic lethality caused by hemorrhaging and clotting in the placenta and surviving embryos die prior to weaning. Mice homozygous for another null allele undergo growth arrest after hatching and apoptosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	A	T	8: 87,293,168 (GRCm39)	Y7N	probably damaging	Het
Adcy1	A	C	11: 7,111,351 (GRCm39)	I881L	probably benign	Het
Aftph	T	C	11: 20,676,994 (GRCm39)	D205G	probably damaging	Het
Aldh7a1	T	A	18: 56,667,325 (GRCm39)	N316Y	possibly damaging	Het
Ankrd36	A	G	11: 5,639,340 (GRCm39)		probably benign	Het
Ccdc88a	T	G	11: 29,448,416 (GRCm39)	N1465K	possibly damaging	Het
Ccpg1	G	A	9: 72,920,326 (GRCm39)	S647N	probably benign	Het
Cep70	T	A	9: 99,163,128 (GRCm39)	L325Q	probably damaging	Het
Cfap46	A	G	7: 139,193,423 (GRCm39)		probably null	Het
Cftr	C	T	6: 18,226,128 (GRCm39)	Q359*	probably null	Het
Chrne	A	T	11: 70,505,913 (GRCm39)	N457K	possibly damaging	Het
Cntn2	A	G	1: 132,451,415 (GRCm39)	I438T	probably benign	Het
Cntn4	T	C	6: 106,158,765 (GRCm39)	L10P	possibly damaging	Het
Copg1	G	T	6: 87,867,189 (GRCm39)	M87I	possibly damaging	Het
Cyfip1	A	T	7: 55,574,883 (GRCm39)	M1045L	possibly damaging	Het
Cyp2c29	C	T	19: 39,318,816 (GRCm39)	P432L	probably damaging	Het
Dcaf11	T	A	14: 55,800,833 (GRCm39)	D96E	probably damaging	Het
Dmxl2	A	G	9: 54,286,041 (GRCm39)	S2715P	probably benign	Het
Dnhd1	G	A	7: 105,363,644 (GRCm39)	E4069K	possibly damaging	Het
Dpy19l4	T	A	4: 11,289,721 (GRCm39)	N330I	probably damaging	Het
Dpy19l4	G	T	4: 11,304,014 (GRCm39)	A132D	probably damaging	Het
Duox2	A	G	2: 122,125,617 (GRCm39)	V330A	probably benign	Het
Dusp11	T	C	6: 85,924,587 (GRCm39)	*322W	probably null	Het
Dusp8	T	A	7: 141,643,730 (GRCm39)	Q61L	possibly damaging	Het
Eml3	G	A	19: 8,916,638 (GRCm39)	G720S	probably damaging	Het
F11	A	G	8: 45,699,833 (GRCm39)	S418P	probably damaging	Het
Fam91a1	G	A	15: 58,320,243 (GRCm39)	S645N	probably benign	Het
Fat2	G	A	11: 55,158,482 (GRCm39)	T3412I	probably benign	Het
Fbxo38	A	G	18: 62,674,042 (GRCm39)	M13T	probably benign	Het
Fbxo48	G	T	11: 16,904,329 (GRCm39)	L160F	possibly damaging	Het
Gm10134	T	A	2: 28,396,372 (GRCm39)		probably benign	Het
Gm11787	T	C	4: 3,511,795 (GRCm39)		noncoding transcript	Het
Gpatch8	A	T	11: 102,399,053 (GRCm39)		probably null	Het
Gucy2g	G	A	19: 55,203,548 (GRCm39)	A750V	probably damaging	Het
Hephl1	T	C	9: 14,988,150 (GRCm39)	T653A	possibly damaging	Het
Herc3	T	A	6: 58,851,263 (GRCm39)	M504K	probably damaging	Het
Hmcn2	A	G	2: 31,350,333 (GRCm39)	T5077A	probably benign	Het
Ifitm3	T	C	7: 140,590,554 (GRCm39)	N2S	probably benign	Het
Ighe	T	C	12: 113,235,092 (GRCm39)	H356R	probably benign	Het
Ighv10-3	T	A	12: 114,487,125 (GRCm39)	M99L	probably benign	Het
Izumo4	C	A	10: 80,538,639 (GRCm39)	C30*	probably null	Het
Jag1	A	T	2: 136,937,464 (GRCm39)	H303Q	possibly damaging	Het
Kif24	T	C	4: 41,395,373 (GRCm39)	E500G	probably benign	Het
Kng1	A	T	16: 22,897,842 (GRCm39)	D414V	probably damaging	Het
Loxhd1	A	C	18: 77,451,308 (GRCm39)	D410A	probably damaging	Het
Ltn1	T	C	16: 87,212,899 (GRCm39)	K554R	possibly damaging	Het
Ly75	A	G	2: 60,133,985 (GRCm39)	C1547R	probably damaging	Het
Ms4a6d	A	T	19: 11,564,500 (GRCm39)	S124T	possibly damaging	Het
Mtcl3	A	G	10: 29,072,766 (GRCm39)	D686G	probably benign	Het
Mtfr2	A	G	10: 20,233,448 (GRCm39)	D339G	probably damaging	Het
Myh10	T	A	11: 68,692,434 (GRCm39)	L1369Q	probably damaging	Het
Myh11	A	T	16: 14,025,872 (GRCm39)	V1366D	possibly damaging	Het
Nadsyn1	A	G	7: 143,357,023 (GRCm39)	V491A	possibly damaging	Het
Nav3	T	C	10: 109,688,966 (GRCm39)	N437S	probably benign	Het
Ncf1	A	G	5: 134,250,659 (GRCm39)	L373P	probably damaging	Het
Neb	A	T	2: 52,079,873 (GRCm39)	I85N	probably damaging	Het
Nktr	A	G	9: 121,577,659 (GRCm39)	K576E	probably benign	Het
Nmur2	T	A	11: 55,931,040 (GRCm39)	I224F	probably damaging	Het
Oas3	A	G	5: 120,895,055 (GRCm39)	F978S	probably damaging	Het
Or10ag53	C	T	2: 87,082,827 (GRCm39)	P182L	probably benign	Het
Or10ak9	T	C	4: 118,726,772 (GRCm39)	S264P	probably damaging	Het
Or2r3	T	A	6: 42,448,186 (GRCm39)	I309F	probably benign	Het
Or2t48	A	T	11: 58,420,308 (GRCm39)	M168K	probably damaging	Het
Or5p60	T	C	7: 107,724,375 (GRCm39)	T32A	probably benign	Het
Pcyox1	A	T	6: 86,369,336 (GRCm39)		probably null	Het
Pdcd7	G	A	9: 65,265,974 (GRCm39)	W477*	probably null	Het
Pitpnm1	T	C	19: 4,153,435 (GRCm39)	F197S	probably damaging	Het
Plce1	C	A	19: 38,748,535 (GRCm39)	N1755K	probably damaging	Het
Pnpla7	C	A	2: 24,931,031 (GRCm39)	P882Q	probably damaging	Het
Pold2	A	G	11: 5,826,760 (GRCm39)	L58P	probably damaging	Het
Pomt1	C	G	2: 32,134,311 (GRCm39)	Y277*	probably null	Het
Pou4f2	A	G	8: 79,162,958 (GRCm39)	Y26H	unknown	Het
Pphln1-ps1	T	G	16: 13,495,622 (GRCm39)	N240K	probably benign	Het
Ppm1e	A	T	11: 87,249,377 (GRCm39)	L118Q	possibly damaging	Het
Pramel34	C	T	5: 93,785,607 (GRCm39)	M224I	possibly damaging	Het
Prdx2	T	A	8: 85,698,302 (GRCm39)	Y164*	probably null	Het
Prkra	T	G	2: 76,469,622 (GRCm39)	T146P	probably damaging	Het
Prpf8	A	G	11: 75,386,625 (GRCm39)	D1038G	probably damaging	Het
Rab4a	A	T	8: 124,554,113 (GRCm39)	I16L	probably benign	Het
Rai2	A	G	X: 160,561,636 (GRCm39)	N363S	probably benign	Het
Ranbp17	A	T	11: 33,169,241 (GRCm39)	V991D	possibly damaging	Het
Rimbp2	G	A	5: 128,865,656 (GRCm39)	T557M	probably benign	Het
Rmi1	G	A	13: 58,557,280 (GRCm39)	G510R	probably damaging	Het
Sdad1	A	G	5: 92,434,684 (GRCm39)	*687Q	probably null	Het
Sema6d	T	C	2: 124,506,166 (GRCm39)	L720P	probably damaging	Het
Setx	T	G	2: 29,024,045 (GRCm39)		probably null	Het
Sgsm3	T	C	15: 80,892,200 (GRCm39)	V256A	probably benign	Het
Slc28a2b	C	A	2: 122,353,259 (GRCm39)	L480I	probably benign	Het
Sppl2c	T	A	11: 104,078,127 (GRCm39)	I309K	possibly damaging	Het
Stard9	A	G	2: 120,531,111 (GRCm39)	E2456G	probably damaging	Het
Strn3	C	G	12: 51,694,803 (GRCm39)	R320P	probably damaging	Het
Supv3l1	A	T	10: 62,266,375 (GRCm39)	N600K	possibly damaging	Het
Syne2	T	A	12: 76,146,112 (GRCm39)	S6377T	possibly damaging	Het
Tas2r123	A	T	6: 132,824,190 (GRCm39)	H29L	probably benign	Het
Tbl3	C	T	17: 24,924,944 (GRCm39)	V52M	possibly damaging	Het
Tcf20	A	T	15: 82,739,910 (GRCm39)	S514T	possibly damaging	Het
Tgm4	A	G	9: 122,885,559 (GRCm39)	Y367C	probably damaging	Het
Tle1	C	T	4: 72,060,081 (GRCm39)	V258M	probably damaging	Het
Tln1	C	T	4: 43,540,661 (GRCm39)	V1447I	probably benign	Het
Tnfrsf11b	C	T	15: 54,141,622 (GRCm39)	A8T	probably benign	Het
Trim80	A	T	11: 115,338,843 (GRCm39)	T558S	probably benign	Het
Trmt6	C	A	2: 132,650,703 (GRCm39)	A302S	probably benign	Het
Tsen15	C	T	1: 152,259,131 (GRCm39)	V76I	probably damaging	Het
Ttc17	A	T	2: 94,133,985 (GRCm39)	W1067R	probably damaging	Het
Ucn3	A	T	13: 3,991,474 (GRCm39)	F59L	probably benign	Het
Ulk3	T	A	9: 57,498,023 (GRCm39)	I108N	possibly damaging	Het
Vmn2r94	A	C	17: 18,464,728 (GRCm39)	Y521D	probably damaging	Het
Vps45	T	C	3: 95,965,086 (GRCm39)	M1V	probably null	Het
Vta1	C	A	10: 14,581,143 (GRCm39)	L21F	probably damaging	Het
Zdhhc21	C	T	4: 82,765,929 (GRCm39)	G2D	probably damaging	Het
Zfp169	A	T	13: 48,643,751 (GRCm39)	C459S	possibly damaging	Het
Zfp90	C	T	8: 107,152,000 (GRCm39)	T571M	probably damaging	Het
Zswim8	A	T	14: 20,768,939 (GRCm39)	N1119I	possibly damaging	Het

Other mutations in Tbp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02260:Tbp	APN	17	15,724,878 (GRCm39)	missense	probably damaging	1.00
R2424:Tbp	UTSW	17	15,733,795 (GRCm39)	missense	possibly damaging	0.94
R6343:Tbp	UTSW	17	15,721,351 (GRCm39)	splice site	probably null

Predicted Primers

PCR Primer
(F):5'- GTGAGAATATCTGGTATGGAGCAC -3'
(R):5'- GATACGCATGGTATATACCCATCTTG -3'

Sequencing Primer
(F):5'- GGAGCACTTTTTGGACTAAAGTCAGC -3'
(R):5'- ACCCATCTTGTTGATATTGAGAAAC -3'

Posted On

2016-08-04