Mutagenetix > Incidental Mutation

Incidental Mutation 'R8400:Tdrd1'

647841

Institutional Source

Beutler Lab

Gene Symbol

Tdrd1

Ensembl Gene

ENSMUSG00000025081

Gene Name

tudor domain containing 1

Synonyms

MTR-1

MMRRC Submission

Accession Numbers

Genbank: NM_001002238

Is this an essential gene?

Possibly non essential (E-score: 0.329) question?

Stock #

R8400 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

56826209-56870012 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 56848649 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 472 (V472M)

Ref Sequence

ENSEMBL: ENSMUSP00000077785 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000078723] [ENSMUST00000111604] [ENSMUST00000111606] [ENSMUST00000121249]

AlphaFold

Q99MV1

PDB Structure

Structure of extended Tudor domain TD3 from mouse TDRD1 in complex with MILI peptide containing dimethylarginine 45. [X-RAY DIFFRACTION]
Structure of extended Tudor domain TD3 from mouse TDRD1 [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000078723
AA Change: V472M

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000077785
Gene: ENSMUSG00000025081
AA Change: V472M

Domain	Start	End	E-Value	Type
low complexity region	75	86	N/A	INTRINSIC
low complexity region	103	117	N/A	INTRINSIC
Pfam:zf-MYND	163	199	3.5e-13	PFAM
TUDOR	306	365	6.45e-11	SMART
TUDOR	537	593	4.88e-11	SMART
low complexity region	698	714	N/A	INTRINSIC
low complexity region	728	739	N/A	INTRINSIC
TUDOR	755	813	3.97e-11	SMART
TUDOR	981	1038	1.27e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000111604
AA Change: V472M

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000107231
Gene: ENSMUSG00000025081
AA Change: V472M

Domain	Start	End	E-Value	Type
low complexity region	75	86	N/A	INTRINSIC
low complexity region	103	117	N/A	INTRINSIC
Pfam:zf-MYND	163	199	3.5e-13	PFAM
TUDOR	306	365	6.45e-11	SMART
TUDOR	537	593	4.88e-11	SMART
low complexity region	698	714	N/A	INTRINSIC
low complexity region	728	739	N/A	INTRINSIC
TUDOR	755	813	3.97e-11	SMART
TUDOR	981	1038	1.27e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000111606
AA Change: V472M

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000107233
Gene: ENSMUSG00000025081
AA Change: V472M

Domain	Start	End	E-Value	Type
low complexity region	75	86	N/A	INTRINSIC
low complexity region	103	117	N/A	INTRINSIC
Pfam:zf-MYND	163	199	3.5e-13	PFAM
TUDOR	306	365	6.45e-11	SMART
TUDOR	537	593	4.88e-11	SMART
low complexity region	698	714	N/A	INTRINSIC
low complexity region	728	739	N/A	INTRINSIC
TUDOR	755	813	3.97e-11	SMART
TUDOR	981	1038	1.27e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000121249
AA Change: V472M

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000112786
Gene: ENSMUSG00000025081
AA Change: V472M

Domain	Start	End	E-Value	Type
low complexity region	75	86	N/A	INTRINSIC
low complexity region	103	117	N/A	INTRINSIC
Pfam:zf-MYND	163	199	9.9e-13	PFAM
TUDOR	306	365	6.45e-11	SMART
TUDOR	537	593	4.88e-11	SMART
low complexity region	698	714	N/A	INTRINSIC
low complexity region	728	739	N/A	INTRINSIC
TUDOR	755	813	3.97e-11	SMART
TUDOR	981	1038	1.27e-9	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is similar to a mouse gene that encodes a tudor domain protein. Alternatively spliced transcript variants have been described but their full length sequences have not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Male homozygous mice are sterile, displaying postnatal spermatogenic defects. Females are fertile. [provided by MGI curators]

Allele List at MGI

All alleles(3) : Targeted, knock-out(1) Targeted, other(2)

Other mutations in this stock

Total: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	G	A	11: 9,293,925	M1929I	probably benign	Het
Abca13	T	C	11: 9,298,218	I2655T	probably damaging	Het
Acad10	A	G	5: 121,626,205	V887A	possibly damaging	Het
Acot10	T	C	15: 20,666,172	E161G	possibly damaging	Het
Astn1	C	T	1: 158,657,100	P919L	probably benign	Het
Atp1a4	T	A	1: 172,234,494	D688V	probably damaging	Het
C4bp	C	A	1: 130,636,747	C400F	probably damaging	Het
Col6a6	A	C	9: 105,774,796	D1005E	probably damaging	Het
Csnk1g3	C	T	18: 53,953,288	R422C	probably benign	Het
Cutc	T	C	19: 43,753,205	S15P	probably benign	Het
Dgkb	T	C	12: 38,602,838		probably null	Het
Disc1	T	C	8: 125,232,993	V748A	probably benign	Het
Dmbt1	C	G	7: 131,082,587	D778E	unknown	Het
Dmxl2	T	C	9: 54,383,753	Y2471C	probably benign	Het
Fam185a	T	A	5: 21,438,816	N243K	probably benign	Het
Fchsd2	A	T	7: 101,253,573	Q386L	possibly damaging	Het
Gm904	C	A	13: 50,643,417	P49Q	probably damaging	Het
H2-Q10	C	T	17: 35,470,477	R59C	probably damaging	Het
Ier5l	A	G	2: 30,473,093	Y307H	possibly damaging	Het
Kmt2e	C	A	5: 23,497,092	T906K	probably benign	Het
Kndc1	C	T	7: 139,913,518	R467W	probably damaging	Het
Muc5ac	C	A	7: 141,810,476	T2508K	probably damaging	Het
Nlrp9a	A	T	7: 26,565,006	M784L	probably benign	Het
Nlrp9b	T	A	7: 20,024,012	C391*	probably null	Het
Nubp2	A	C	17: 24,884,465	M146R	probably damaging	Het
Olfr1295	A	T	2: 111,565,402	L14H	probably damaging	Het
Olfr1359	G	A	13: 21,703,915	V305M	probably benign	Het
Olfr1419	T	A	19: 11,871,214	M1L	probably damaging	Het
Olfr43	C	T	11: 74,206,395	V274M	possibly damaging	Het
Olfr694	T	A	7: 106,689,669	S21C	probably benign	Het
Olfr857	A	T	9: 19,713,093	N89Y	probably benign	Het
Otud1	T	C	2: 19,658,378	V106A	possibly damaging	Het
Pcdhac1	T	A	18: 37,092,400	Y755*	probably null	Het
Pkd1l3	C	T	8: 109,623,888	P455L	possibly damaging	Het
Ptprb	GAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT	GAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT	10: 116,283,572		probably benign	Het
Samhd1	T	C	2: 157,099,433	E648G	probably benign	Het
Smarca5	T	C	8: 80,709,127	T794A	probably benign	Het
Spc24	A	T	9: 21,757,730	L87H	probably damaging	Het
Sppl2b	TGTCACAGGT	TGT	10: 80,866,069		probably null	Het
Stra6l	G	A	4: 45,864,905	R77Q	probably damaging	Het
Tsc2	A	T	17: 24,604,987	I948K	possibly damaging	Het
Ttc39d	T	C	17: 80,216,005	V31A	probably benign	Het
Vmn1r158	A	T	7: 22,789,880	C301*	probably null	Het
Vmn2r22	A	T	6: 123,637,527	L368*	probably null	Het
Vmn2r79	A	G	7: 87,002,100	T236A	probably benign	Het
Vwa1	T	C	4: 155,772,768	H191R	probably benign	Het
Zdbf2	T	A	1: 63,304,976	V838E	possibly damaging	Het

Other mutations in Tdrd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00423:Tdrd1	APN	19	56851464	missense	possibly damaging	0.51
IGL01366:Tdrd1	APN	19	56855302	missense	probably benign	0.00
IGL01569:Tdrd1	APN	19	56834409	missense	probably damaging	1.00
IGL02691:Tdrd1	APN	19	56843852	missense	probably damaging	0.99
3-1:Tdrd1	UTSW	19	56861695	missense	probably benign
R0081:Tdrd1	UTSW	19	56831271	missense	probably benign	0.16
R0139:Tdrd1	UTSW	19	56843198	missense	probably benign	0.00
R0254:Tdrd1	UTSW	19	56842566	missense	probably benign	0.02
R0686:Tdrd1	UTSW	19	56856051	missense	probably damaging	1.00
R0735:Tdrd1	UTSW	19	56865978	nonsense	probably null
R0740:Tdrd1	UTSW	19	56839099	missense	probably damaging	1.00
R1241:Tdrd1	UTSW	19	56861760	missense	probably benign
R1294:Tdrd1	UTSW	19	56848776	splice site	probably null
R1508:Tdrd1	UTSW	19	56851358	missense	probably damaging	1.00
R1655:Tdrd1	UTSW	19	56843216	nonsense	probably null
R1708:Tdrd1	UTSW	19	56842289	missense	probably benign	0.13
R1796:Tdrd1	UTSW	19	56837783	missense	probably damaging	0.98
R1840:Tdrd1	UTSW	19	56842312	missense	probably damaging	1.00
R2138:Tdrd1	UTSW	19	56842589	missense	probably benign	0.30
R2201:Tdrd1	UTSW	19	56858661	missense	probably benign	0.14
R2201:Tdrd1	UTSW	19	56858662	missense	probably benign	0.00
R2286:Tdrd1	UTSW	19	56839119	missense	probably benign	0.05
R2443:Tdrd1	UTSW	19	56841354	missense	probably null	0.01
R3001:Tdrd1	UTSW	19	56861750	nonsense	probably null
R3002:Tdrd1	UTSW	19	56861750	nonsense	probably null
R3418:Tdrd1	UTSW	19	56831231	missense	possibly damaging	0.87
R3419:Tdrd1	UTSW	19	56831231	missense	possibly damaging	0.87
R3707:Tdrd1	UTSW	19	56865993	missense	possibly damaging	0.86
R3978:Tdrd1	UTSW	19	56866634	missense	probably benign	0.01
R4077:Tdrd1	UTSW	19	56831073	missense	probably benign	0.22
R4083:Tdrd1	UTSW	19	56843230	missense	probably benign
R4193:Tdrd1	UTSW	19	56851341	nonsense	probably null
R5882:Tdrd1	UTSW	19	56848939	missense	probably damaging	1.00
R6073:Tdrd1	UTSW	19	56843223	nonsense	probably null
R6223:Tdrd1	UTSW	19	56865850	missense	probably damaging	1.00
R6240:Tdrd1	UTSW	19	56841335	missense	probably benign	0.00
R6953:Tdrd1	UTSW	19	56831371	missense	probably damaging	0.98
R7090:Tdrd1	UTSW	19	56851401	missense	probably benign	0.28
R7643:Tdrd1	UTSW	19	56837708	missense	probably damaging	1.00
R7793:Tdrd1	UTSW	19	56864377	missense	probably damaging	0.99
R7972:Tdrd1	UTSW	19	56848702	missense	probably damaging	0.98
R7993:Tdrd1	UTSW	19	56866005	splice site	probably null
R8076:Tdrd1	UTSW	19	56843835	missense	probably damaging	0.96
R8346:Tdrd1	UTSW	19	56842267	missense	probably benign	0.44
R8553:Tdrd1	UTSW	19	56843152	missense	probably damaging	0.99
R8701:Tdrd1	UTSW	19	56851484	missense	possibly damaging	0.94
R8772:Tdrd1	UTSW	19	56855328	missense	probably damaging	0.99
R8906:Tdrd1	UTSW	19	56842713	missense	probably damaging	0.99
R9222:Tdrd1	UTSW	19	56843247	missense	probably benign	0.38
R9321:Tdrd1	UTSW	19	56860335	missense	probably damaging	1.00
R9665:Tdrd1	UTSW	19	56831140	missense	probably benign	0.04
R9747:Tdrd1	UTSW	19	56858669	missense	probably benign	0.17
R9756:Tdrd1	UTSW	19	56843230	missense	probably benign
X0020:Tdrd1	UTSW	19	56856060	missense	probably damaging	1.00
X0053:Tdrd1	UTSW	19	56865791	missense	possibly damaging	0.85

Predicted Primers

PCR Primer
(F):5'- TGATGCAGAGCTCCCTTTCTG -3'
(R):5'- GCATGCTGAGTCTCATGGAAC -3'

Sequencing Primer
(F):5'- TTTCTGAAGGTCCAGCAGC -3'
(R):5'- TGGAACACTTTCTCGCAACAC -3'

Posted On

2020-09-02