Mutagenetix > Incidental Mutation

Incidental Mutation 'R5488:Tardbp'

430451

Institutional Source

Beutler Lab

Gene Symbol

Tardbp

Ensembl Gene

ENSMUSG00000041459

Gene Name

TAR DNA binding protein

Synonyms

Tdp43, TDP-43, 1190002A23Rik

MMRRC Submission

043049-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5488 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

148696839-148711476 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 148703097 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 289 (F289S)

Ref Sequence

ENSEMBL: ENSMUSP00000081142 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045180] [ENSMUST00000052060] [ENSMUST00000084125] [ENSMUST00000095719] [ENSMUST00000105699] [ENSMUST00000105700] [ENSMUST00000105702] [ENSMUST00000186947] [ENSMUST00000172073] [ENSMUST00000186711] [ENSMUST00000186729] [ENSMUST00000140897] [ENSMUST00000165113] [ENSMUST00000188134] [ENSMUST00000187939] [ENSMUST00000185673] [ENSMUST00000190696] [ENSMUST00000189048] [ENSMUST00000190552] [ENSMUST00000191450]

AlphaFold

Q921F2

PDB Structure

Crystal structure of mouse TDP-43 RRM2 domain in complex with DNA [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000045180

SMART Domains

Protein: ENSMUSP00000038113
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000052060

SMART Domains

Protein: ENSMUSP00000049729
Gene: ENSMUSG00000028979

Domain	Start	End	E-Value	Type
CUB	18	137	4.71e-30	SMART
EGF_CA	138	181	4.32e-10	SMART
CUB	184	296	4.29e-33	SMART
CCP	300	361	1.79e-12	SMART
CCP	366	429	5.4e-7	SMART
Tryp_SPc	443	678	1.3e-82	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000084125
AA Change: F289S

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000081142
Gene: ENSMUSG00000041459
AA Change: F289S

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART
low complexity region	273	316	N/A	INTRINSIC
low complexity region	321	329	N/A	INTRINSIC
low complexity region	342	358	N/A	INTRINSIC
low complexity region	368	380	N/A	INTRINSIC
low complexity region	386	404	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000095719

SMART Domains

Protein: ENSMUSP00000093386
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART
low complexity region	274	285	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105699

SMART Domains

Protein: ENSMUSP00000101324
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105700

SMART Domains

Protein: ENSMUSP00000101325
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105702

SMART Domains

Protein: ENSMUSP00000101327
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000186947
AA Change: F232S

SMART Domains

Protein: ENSMUSP00000140529
Gene: ENSMUSG00000041459
AA Change: F232S

Domain	Start	End	E-Value	Type
RRM	105	176	5.8e-20	SMART
low complexity region	215	243	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172073

SMART Domains

Protein: ENSMUSP00000130963
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART
low complexity region	274	285	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186711

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186317

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187937

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188380

Predicted Effect

probably benign
Transcript: ENSMUST00000185824

Predicted Effect

probably benign
Transcript: ENSMUST00000186729

SMART Domains

Protein: ENSMUSP00000139547
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
Pfam:RRM_1	1	37	1.8e-4	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000140897

SMART Domains

Protein: ENSMUSP00000135135
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
Blast:RRM_2	1	28	2e-13	BLAST
RRM	44	110	3e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000165113

SMART Domains

Protein: ENSMUSP00000129342
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000188134

SMART Domains

Protein: ENSMUSP00000139476
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000147391

Predicted Effect

probably benign
Transcript: ENSMUST00000187939

SMART Domains

Protein: ENSMUSP00000140928
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	18	84	3e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000185673

SMART Domains

Protein: ENSMUSP00000141010
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
Pfam:RRM_1	106	149	3e-12	PFAM
Pfam:RRM_6	106	149	1.3e-6	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189041

Predicted Effect

probably benign
Transcript: ENSMUST00000190696

SMART Domains

Protein: ENSMUSP00000139637
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
Blast:RRM_2	55	79	8e-11	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000188488

Predicted Effect

probably benign
Transcript: ENSMUST00000189048

SMART Domains

Protein: ENSMUSP00000140364
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	1.38e-17	SMART
RRM	192	258	7.03e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000190287

Predicted Effect

probably benign
Transcript: ENSMUST00000190552

SMART Domains

Protein: ENSMUSP00000141052
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM_2	1	56	6.1e-4	SMART
RRM	72	138	3e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000191450

SMART Domains

Protein: ENSMUSP00000140832
Gene: ENSMUSG00000041459

Domain	Start	End	E-Value	Type
RRM	105	176	5.8e-20	SMART
RRM	192	258	3e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000191378

Predicted Effect

probably benign
Transcript: ENSMUST00000190630

Meta Mutation Damage Score

0.0692

Coding Region Coverage

1x: 98.2%
3x: 97.2%
10x: 95.1%
20x: 90.5%

Validation Efficiency

97% (58/60)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. The protein encoded by this gene is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous deficient mice display embryonic lethality before somite formation with impaired inner cell mass proliferation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	A	7: 119,851,473 (GRCm39)	V817D	probably damaging	Het
Abca5	A	G	11: 110,183,009 (GRCm39)	V1016A	probably benign	Het
Ano2	G	T	6: 126,016,216 (GRCm39)	M916I	possibly damaging	Het
Aqr	T	C	2: 113,963,554 (GRCm39)	N632S	probably damaging	Het
Cd48	G	A	1: 171,523,273 (GRCm39)	V39I	possibly damaging	Het
Cdcp3	A	G	7: 130,848,324 (GRCm39)	D710G	probably damaging	Het
Cdk17	A	G	10: 93,068,274 (GRCm39)	T344A	probably damaging	Het
Chd8	A	T	14: 52,450,505 (GRCm39)		probably benign	Het
Col4a1	A	T	8: 11,362,550 (GRCm39)		probably benign	Het
Col9a3	G	A	2: 180,258,318 (GRCm39)	R579H	probably damaging	Het
Cripto	G	A	9: 110,772,265 (GRCm39)	R44C	probably benign	Het
Cyp2c69	T	G	19: 39,839,603 (GRCm39)	Q340P	probably null	Het
D630003M21Rik	T	A	2: 158,058,941 (GRCm39)	T320S	probably benign	Het
D630045J12Rik	A	T	6: 38,173,782 (GRCm39)	S129T	possibly damaging	Het
Eif4a3l1	C	G	6: 136,306,555 (GRCm39)	R339G	probably damaging	Het
Fam13a	A	T	6: 59,001,303 (GRCm39)	L8Q	probably null	Het
Fam83b	T	C	9: 76,452,881 (GRCm39)	N62S	probably benign	Het
Foxred1	A	T	9: 35,121,266 (GRCm39)	V94E	probably damaging	Het
Gprc5a	T	C	6: 135,055,868 (GRCm39)	V105A	probably damaging	Het
Gvin3	T	A	7: 106,200,797 (GRCm39)		noncoding transcript	Het
Itga2	A	T	13: 114,979,971 (GRCm39)	W1077R	probably damaging	Het
Kat6b	A	G	14: 21,719,332 (GRCm39)	D1228G	probably damaging	Het
Kctd3	A	G	1: 188,713,563 (GRCm39)	Y391H	probably damaging	Het
Kdelr2	T	A	5: 143,389,784 (GRCm39)	I23N	probably damaging	Het
Kmt2a	A	T	9: 44,752,335 (GRCm39)		probably benign	Het
Lao1	A	G	4: 118,824,566 (GRCm39)	E216G	probably damaging	Het
Mark4	G	T	7: 19,163,532 (GRCm39)		probably null	Het
Mcm10	A	G	2: 4,996,929 (GRCm39)	W851R	probably damaging	Het
Mettl21e	T	C	1: 44,257,276 (GRCm39)	Y14C	probably benign	Het
Miga1	CACAACAACAACAACAACA	CACAACAACAACAACA	3: 152,039,083 (GRCm39)		probably benign	Het
Mmp20	A	G	9: 7,643,958 (GRCm39)		probably null	Het
Nlrp5	A	T	7: 23,117,359 (GRCm39)	D361V	probably benign	Het
Nrip3	T	C	7: 109,361,045 (GRCm39)	T210A	probably damaging	Het
Or12d2	T	C	17: 37,624,559 (GRCm39)	T239A	probably damaging	Het
Or52s1b	T	C	7: 102,822,658 (GRCm39)	Y62C	probably damaging	Het
Pcdh10	G	A	3: 45,335,803 (GRCm39)	G706S	probably damaging	Het
Pdzd2	G	A	15: 12,382,762 (GRCm39)	P1197L	probably benign	Het
Pfkfb3	T	C	2: 11,489,480 (GRCm39)	S273G	probably benign	Het
Pkn3	T	C	2: 29,978,596 (GRCm39)		probably null	Het
Rab40c	G	A	17: 26,109,643 (GRCm39)	T78I	probably damaging	Het
Rec8	A	T	14: 55,860,283 (GRCm39)	Q291L	probably benign	Het
Robo4	CGG	CG	9: 37,322,786 (GRCm39)		probably null	Het
Sart3	A	G	5: 113,909,441 (GRCm39)	W86R	probably damaging	Het
Slc6a11	A	G	6: 114,220,855 (GRCm39)	D462G	probably damaging	Het
Syne2	A	G	12: 75,934,946 (GRCm39)	T143A	probably benign	Het
Tdpoz1	T	A	3: 93,577,974 (GRCm39)	Y270F	possibly damaging	Het
Tmem117	ACCC	ACC	15: 94,992,698 (GRCm39)		probably null	Het
Trim43a	A	T	9: 88,464,229 (GRCm39)	I47F	probably damaging	Het
Vim	A	T	2: 13,580,392 (GRCm39)	T202S	probably benign	Het
Vps13b	A	T	15: 35,770,688 (GRCm39)	I2044L	probably benign	Het
Wdr5	T	G	2: 27,415,165 (GRCm39)	D192E	probably damaging	Het
Zmym2	A	G	14: 57,193,712 (GRCm39)	K1176E	possibly damaging	Het

Other mutations in Tardbp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01472:Tardbp	APN	4	148,706,521 (GRCm39)	missense	probably benign	0.03
IGL02569:Tardbp	APN	4	148,703,639 (GRCm39)	critical splice donor site	probably null
R4428:Tardbp	UTSW	4	148,709,659 (GRCm39)	missense	possibly damaging	0.88
R4690:Tardbp	UTSW	4	148,697,078 (GRCm39)	makesense	probably null
R4824:Tardbp	UTSW	4	148,702,050 (GRCm39)	missense	probably benign	0.33
R4925:Tardbp	UTSW	4	148,703,108 (GRCm39)	missense	probably benign	0.11
R5057:Tardbp	UTSW	4	148,703,813 (GRCm39)	critical splice acceptor site	probably null
R5137:Tardbp	UTSW	4	148,706,494 (GRCm39)	missense	possibly damaging	0.77
R5833:Tardbp	UTSW	4	148,702,117 (GRCm39)	missense	probably damaging	1.00
R8164:Tardbp	UTSW	4	148,703,060 (GRCm39)	missense	probably benign	0.00
R8862:Tardbp	UTSW	4	148,702,755 (GRCm39)	missense	possibly damaging	0.73
R8905:Tardbp	UTSW	4	148,705,093 (GRCm39)	missense	probably benign	0.01
R9664:Tardbp	UTSW	4	148,709,751 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TCTGCTGGCTGGCTAACATG -3'
(R):5'- AACTAAAGGCTGCTGGTTGGG -3'

Sequencing Primer
(F):5'- GGCTAACATGCCCATCATACC -3'
(R):5'- GGTTTAAGTAAATTGCCTGTTTTTCC -3'

Posted On

2016-10-05