Mutagenetix > Incidental Mutation

Incidental Mutation 'R1459:Matr3'

162012

Institutional Source

Beutler Lab

Gene Symbol

Matr3

Ensembl Gene

ENSMUSG00000037236

Gene Name

matrin 3

Synonyms

D030046F20Rik, 2810017I02Rik, 1110061A14Rik

MMRRC Submission

039514-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.959) question?

Stock #

R1459 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35695191-35726888 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 35717709 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 302 (D302E)

Ref Sequence

ENSEMBL: ENSMUSP00000140853 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000166793] [ENSMUST00000186796] [ENSMUST00000187389] [ENSMUST00000187793] [ENSMUST00000188275] [ENSMUST00000188767] [ENSMUST00000190029] [ENSMUST00000190121] [ENSMUST00000190653]

AlphaFold

Q8K310

Predicted Effect

probably benign
Transcript: ENSMUST00000166793
AA Change: D640E

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000125761
Gene: ENSMUSG00000037236
AA Change: D640E

Domain	Start	End	E-Value	Type
low complexity region	23	32	N/A	INTRINSIC
low complexity region	52	65	N/A	INTRINSIC
low complexity region	69	85	N/A	INTRINSIC
ZnF_U1	288	322	4.47e-6	SMART
ZnF_C2H2	291	315	2.12e1	SMART
low complexity region	351	361	N/A	INTRINSIC
low complexity region	371	386	N/A	INTRINSIC
RRM	399	469	7.74e-3	SMART
RRM	497	567	5.63e-9	SMART
low complexity region	650	675	N/A	INTRINSIC
low complexity region	710	718	N/A	INTRINSIC
ZnF_U1	797	832	1.87e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000186796
AA Change: D302E

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000140128
Gene: ENSMUSG00000037236
AA Change: D302E

Domain	Start	End	E-Value	Type
low complexity region	13	23	N/A	INTRINSIC
low complexity region	33	48	N/A	INTRINSIC
RRM	61	131	3.2e-5	SMART
RRM	159	229	2.4e-11	SMART
low complexity region	312	337	N/A	INTRINSIC
low complexity region	372	380	N/A	INTRINSIC
ZnF_U1	459	494	1.1e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000187389
AA Change: D640E

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000139745
Gene: ENSMUSG00000037236
AA Change: D640E

Domain	Start	End	E-Value	Type
low complexity region	23	32	N/A	INTRINSIC
low complexity region	52	65	N/A	INTRINSIC
low complexity region	69	85	N/A	INTRINSIC
ZnF_U1	288	322	4.47e-6	SMART
ZnF_C2H2	291	315	2.12e1	SMART
low complexity region	351	361	N/A	INTRINSIC
low complexity region	371	386	N/A	INTRINSIC
RRM	399	469	7.74e-3	SMART
RRM	497	567	5.63e-9	SMART
low complexity region	650	675	N/A	INTRINSIC
low complexity region	710	718	N/A	INTRINSIC
ZnF_U1	797	832	1.87e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000187793

SMART Domains

Protein: ENSMUSP00000140047
Gene: ENSMUSG00000099703

Domain	Start	End	E-Value	Type
low complexity region	13	23	N/A	INTRINSIC
SCOP:d1lvk_2	42	78	4e-3	SMART
PDB:1X4D\|A	52	102	4e-30	PDB
Blast:RRM	61	102	1e-22	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000188275
AA Change: D352E

PolyPhen 2 Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000140401
Gene: ENSMUSG00000037236
AA Change: D352E

Domain	Start	End	E-Value	Type
low complexity region	63	73	N/A	INTRINSIC
low complexity region	83	98	N/A	INTRINSIC
RRM	111	181	3.2e-5	SMART
RRM	209	279	2.4e-11	SMART
low complexity region	362	387	N/A	INTRINSIC
low complexity region	422	430	N/A	INTRINSIC
ZnF_U1	509	544	1.1e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000188767

SMART Domains

Protein: ENSMUSP00000141027
Gene: ENSMUSG00000037236

Domain	Start	End	E-Value	Type
low complexity region	13	23	N/A	INTRINSIC
low complexity region	33	48	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189019

Predicted Effect

probably benign
Transcript: ENSMUST00000190029
AA Change: D640E

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000140846
Gene: ENSMUSG00000037236
AA Change: D640E

Domain	Start	End	E-Value	Type
low complexity region	23	32	N/A	INTRINSIC
low complexity region	52	65	N/A	INTRINSIC
low complexity region	69	85	N/A	INTRINSIC
ZnF_U1	288	322	4.47e-6	SMART
ZnF_C2H2	291	315	2.12e1	SMART
low complexity region	351	361	N/A	INTRINSIC
low complexity region	371	386	N/A	INTRINSIC
RRM	399	469	7.74e-3	SMART
RRM	497	567	5.63e-9	SMART
low complexity region	650	675	N/A	INTRINSIC
low complexity region	710	718	N/A	INTRINSIC
ZnF_U1	797	832	1.87e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000190121
AA Change: D302E

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000140853
Gene: ENSMUSG00000037236
AA Change: D302E

Domain	Start	End	E-Value	Type
low complexity region	13	23	N/A	INTRINSIC
low complexity region	33	48	N/A	INTRINSIC
RRM	61	131	3.2e-5	SMART
RRM	159	229	2.4e-11	SMART
low complexity region	312	337	N/A	INTRINSIC
low complexity region	372	380	N/A	INTRINSIC
ZnF_U1	459	494	1.1e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000190653
AA Change: D302E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000141135
Gene: ENSMUSG00000037236
AA Change: D302E

Domain	Start	End	E-Value	Type
low complexity region	13	23	N/A	INTRINSIC
low complexity region	33	48	N/A	INTRINSIC
RRM	61	131	3.2e-5	SMART
RRM	159	229	2.4e-11	SMART
low complexity region	312	337	N/A	INTRINSIC
low complexity region	372	380	N/A	INTRINSIC
ZnF_U1	459	494	1.1e-10	SMART

Meta Mutation Damage Score

0.0589

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.3%
20x: 89.5%

Validation Efficiency

96% (87/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a gene-trapped allele are early embryonic lethal. Heterozygotes show congenital heart defects including abnormal heart apex morphology, subaortic ventricular septal defects, double-outlet right ventricle, bicuspid aortic valve, aorta coarctation, and patent ductus arteriosus. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933430I17Rik	C	T	4: 62,450,578 (GRCm39)	R51W	probably damaging	Het
Abcb1a	T	A	5: 8,752,920 (GRCm39)	L557Q	probably damaging	Het
Abcb4	T	C	5: 8,968,662 (GRCm39)	F334L	possibly damaging	Het
Adamts14	T	A	10: 61,034,583 (GRCm39)	T1102S	probably benign	Het
Adamtsl1	T	C	4: 86,344,102 (GRCm39)	Y1719H	probably damaging	Het
Adcyap1	T	C	17: 93,507,550 (GRCm39)		probably null	Het
Ankrd13c	T	A	3: 157,677,947 (GRCm39)	L219Q	probably damaging	Het
Ano3	C	A	2: 110,711,174 (GRCm39)	A97S	probably benign	Het
Apaf1	T	C	10: 90,898,022 (GRCm39)	N245S	probably benign	Het
Apob	A	G	12: 8,056,047 (GRCm39)	T1510A	probably benign	Het
Apob	A	G	12: 8,061,937 (GRCm39)	D3473G	possibly damaging	Het
Arfgap3	G	A	15: 83,191,138 (GRCm39)	T12I	probably benign	Het
Bend4	A	G	5: 67,557,418 (GRCm39)	V466A	probably damaging	Het
Bend7	G	A	2: 4,749,239 (GRCm39)	E119K	probably damaging	Het
Capn5	G	T	7: 97,781,049 (GRCm39)	R243S	possibly damaging	Het
Cd84	A	G	1: 171,679,510 (GRCm39)	I63V	probably benign	Het
Cd86	T	A	16: 36,449,350 (GRCm39)	T16S	probably benign	Het
Cdc42bpb	A	G	12: 111,262,734 (GRCm39)		probably benign	Het
Cep20	G	A	16: 14,122,380 (GRCm39)	T128I	possibly damaging	Het
Cep95	C	T	11: 106,708,781 (GRCm39)	S26L	probably damaging	Het
Cldn19	C	T	4: 119,112,810 (GRCm39)	A14V	probably damaging	Het
Cluap1	T	A	16: 3,755,453 (GRCm39)	M356K	probably damaging	Het
Coq7	C	T	7: 118,109,260 (GRCm39)	G263S	unknown	Het
Ctnnd2	A	C	15: 30,847,445 (GRCm39)	T679P	probably damaging	Het
Dnah10	A	G	5: 124,820,750 (GRCm39)	D528G	possibly damaging	Het
Dvl1	T	A	4: 155,938,476 (GRCm39)	N133K	probably damaging	Het
Efcab7	T	G	4: 99,769,744 (GRCm39)	H550Q	probably null	Het
Fastkd5	C	T	2: 130,456,717 (GRCm39)	M624I	probably damaging	Het
Fbxo42	T	C	4: 140,895,073 (GRCm39)	V12A	probably benign	Het
Gabarapl1	T	A	6: 129,515,635 (GRCm39)	M91K	possibly damaging	Het
Gas7	A	G	11: 67,552,902 (GRCm39)	N154S	probably damaging	Het
Gm21814	T	A	6: 149,483,650 (GRCm39)		noncoding transcript	Het
Gnl3	G	A	14: 30,739,803 (GRCm39)	R12C	probably damaging	Het
Golga2	T	G	2: 32,187,807 (GRCm39)		probably null	Het
Grk3	T	A	5: 113,062,878 (GRCm39)	R656S	probably benign	Het
Gsap	T	A	5: 21,412,236 (GRCm39)		probably benign	Het
H60c	T	C	10: 3,210,240 (GRCm39)	Q103R	probably benign	Het
Hnrnpr	T	A	4: 136,056,755 (GRCm39)	S252T	probably damaging	Het
Itgb4	A	T	11: 115,869,937 (GRCm39)	T40S	probably benign	Het
Krtap27-1	T	C	16: 88,468,302 (GRCm39)	N81D	probably benign	Het
Lilrb4a	T	A	10: 51,367,683 (GRCm39)	L75Q	probably benign	Het
Lrp2	T	A	2: 69,290,821 (GRCm39)	E3546D	probably damaging	Het
Lrp2	T	A	2: 69,313,738 (GRCm39)	D2331V	probably damaging	Het
Lzts2	T	A	19: 45,009,893 (GRCm39)	V9E	probably damaging	Het
Mcoln2	A	G	3: 145,897,979 (GRCm39)		probably null	Het
Metap2	T	C	10: 93,704,811 (GRCm39)	D272G	probably damaging	Het
Mitf	A	G	6: 97,987,428 (GRCm39)	D337G	probably damaging	Het
Mrtfb	T	C	16: 13,219,433 (GRCm39)	V693A	possibly damaging	Het
Msh2	A	G	17: 87,985,771 (GRCm39)	E116G	probably benign	Het
Nlrp10	T	A	7: 108,523,555 (GRCm39)	M642L	probably benign	Het
Noxa1	G	T	2: 24,982,558 (GRCm39)	Q86K	probably benign	Het
Nrap	T	C	19: 56,372,562 (GRCm39)	T48A	probably benign	Het
Nup160	T	A	2: 90,520,494 (GRCm39)	H308Q	probably damaging	Het
Osbpl11	T	C	16: 33,056,699 (GRCm39)	L711P	probably damaging	Het
Osbpl6	A	G	2: 76,385,409 (GRCm39)	N281S	probably benign	Het
Pcnp	C	T	16: 55,844,703 (GRCm39)	E66K	possibly damaging	Het
Phf11	T	A	14: 59,482,227 (GRCm39)	E175D	probably damaging	Het
Pik3cg	A	G	12: 32,254,983 (GRCm39)	Y335H	probably damaging	Het
Plekhg4	T	C	8: 106,108,431 (GRCm39)	L1053S	probably damaging	Het
Plekhh2	G	T	17: 84,918,203 (GRCm39)	E1271*	probably null	Het
Ppp2r2b	T	A	18: 42,871,055 (GRCm39)	Y82F	probably damaging	Het
Prkd3	T	C	17: 79,278,796 (GRCm39)	D430G	probably damaging	Het
Prl7d1	C	T	13: 27,893,240 (GRCm39)	D224N	possibly damaging	Het
Ptpdc1	A	T	13: 48,740,173 (GRCm39)	N419K	possibly damaging	Het
Serinc5	T	A	13: 92,797,695 (GRCm39)		probably null	Het
Sipa1	A	G	19: 5,701,692 (GRCm39)	L981P	probably damaging	Het
Slc16a7	A	T	10: 125,066,489 (GRCm39)	C383*	probably null	Het
Slc19a1	C	G	10: 76,878,369 (GRCm39)	Y301*	probably null	Het
Slc22a14	A	T	9: 119,052,827 (GRCm39)	V14E	possibly damaging	Het
Slpi	C	A	2: 164,196,837 (GRCm39)	C95F	probably damaging	Het
Smurf2	G	A	11: 106,743,333 (GRCm39)	H225Y	possibly damaging	Het
Son	T	C	16: 91,452,230 (GRCm39)	S326P	possibly damaging	Het
Sptb	T	A	12: 76,658,657 (GRCm39)	K1262M	probably benign	Het
Sugp2	T	A	8: 70,696,714 (GRCm39)		probably benign	Het
Tatdn2	T	A	6: 113,687,031 (GRCm39)	H747Q	probably damaging	Het
Tcn2	C	A	11: 3,877,516 (GRCm39)	R44L	probably benign	Het
Tenm3	G	A	8: 48,689,006 (GRCm39)	R2194C	probably damaging	Het
Tnks2	T	A	19: 36,822,931 (GRCm39)		probably benign	Het
Top3a	A	T	11: 60,650,188 (GRCm39)	I120N	probably damaging	Het
Umodl1	T	A	17: 31,201,232 (GRCm39)		probably benign	Het
Umodl1	T	C	17: 31,205,478 (GRCm39)	V662A	probably benign	Het
Ush2a	T	C	1: 188,595,048 (GRCm39)	S3827P	probably benign	Het
Vasn	T	A	16: 4,466,473 (GRCm39)		probably null	Het
Vmn2r69	A	T	7: 85,055,908 (GRCm39)	C743*	probably null	Het
Vmn2r79	C	A	7: 86,687,002 (GRCm39)	H794Q	probably benign	Het

Other mutations in Matr3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01396:Matr3	APN	18	35,721,442 (GRCm39)	missense	probably damaging	1.00
IGL03083:Matr3	APN	18	35,705,471 (GRCm39)	missense	probably damaging	0.96
IGL03117:Matr3	APN	18	35,705,710 (GRCm39)	missense	probably damaging	1.00
IGL03163:Matr3	APN	18	35,705,644 (GRCm39)	missense	probably damaging	0.99
IGL03381:Matr3	APN	18	35,712,078 (GRCm39)	splice site	probably benign
R0456:Matr3	UTSW	18	35,705,917 (GRCm39)	missense	probably damaging	1.00
R1136:Matr3	UTSW	18	35,705,948 (GRCm39)	missense	probably damaging	1.00
R1850:Matr3	UTSW	18	35,715,110 (GRCm39)	missense	probably damaging	1.00
R1929:Matr3	UTSW	18	35,721,378 (GRCm39)	splice site	probably benign
R2185:Matr3	UTSW	18	35,714,278 (GRCm39)	missense	probably damaging	1.00
R2366:Matr3	UTSW	18	35,721,448 (GRCm39)	missense	probably damaging	1.00
R2870:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2870:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2871:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2871:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2872:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2872:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R2873:Matr3	UTSW	18	35,705,349 (GRCm39)	missense	probably benign	0.25
R3908:Matr3	UTSW	18	35,705,894 (GRCm39)	missense	probably damaging	1.00
R4400:Matr3	UTSW	18	35,716,969 (GRCm39)	missense	possibly damaging	0.80
R4417:Matr3	UTSW	18	35,705,171 (GRCm39)	missense	probably damaging	1.00
R4860:Matr3	UTSW	18	35,714,693 (GRCm39)	missense	probably damaging	1.00
R4860:Matr3	UTSW	18	35,714,693 (GRCm39)	missense	probably damaging	1.00
R4881:Matr3	UTSW	18	35,705,428 (GRCm39)	missense	probably damaging	1.00
R4908:Matr3	UTSW	18	35,705,754 (GRCm39)	missense	probably damaging	0.96
R5084:Matr3	UTSW	18	35,715,135 (GRCm39)	missense	probably damaging	0.99
R5660:Matr3	UTSW	18	35,705,147 (GRCm39)	missense	probably damaging	0.99
R5709:Matr3	UTSW	18	35,715,015 (GRCm39)	missense	probably damaging	1.00
R5779:Matr3	UTSW	18	35,717,575 (GRCm39)	missense	possibly damaging	0.81
R5876:Matr3	UTSW	18	35,720,791 (GRCm39)	missense	probably benign
R6392:Matr3	UTSW	18	35,717,894 (GRCm39)	missense	probably benign	0.07
R7062:Matr3	UTSW	18	35,712,072 (GRCm39)	critical splice donor site	probably null
R7156:Matr3	UTSW	18	35,705,974 (GRCm39)	missense	probably damaging	0.98
R7228:Matr3	UTSW	18	35,695,537 (GRCm39)	missense	unknown
R7389:Matr3	UTSW	18	35,717,638 (GRCm39)	missense	probably benign
R8940:Matr3	UTSW	18	35,705,640 (GRCm39)	missense	probably damaging	0.98
R9071:Matr3	UTSW	18	35,705,803 (GRCm39)	missense	possibly damaging	0.94
R9159:Matr3	UTSW	18	35,712,355 (GRCm39)	missense	possibly damaging	0.71
R9205:Matr3	UTSW	18	35,720,774 (GRCm39)	missense	probably benign	0.08
R9587:Matr3	UTSW	18	35,717,876 (GRCm39)	missense	probably null	0.13

Predicted Primers

PCR Primer
(F):5'- TCCACAATCAAAATGTCTCTTTGCAGGA -3'
(R):5'- TCTGGGTCTCACTTCATTGAACCTCTAA -3'

Sequencing Primer
(F):5'- GTCTCTTTGCAGGAAAAGATCC -3'
(R):5'- tgtactcttctggggtgtttg -3'

Posted On

2014-03-14