Mutagenetix > Incidental Mutation

Incidental Mutation 'R5256:Syne3'

399699

Institutional Source

Beutler Lab

Gene Symbol

Syne3

Ensembl Gene

ENSMUSG00000054150

Gene Name

spectrin repeat containing, nuclear envelope family member 3

Synonyms

4831426I19Rik, nesprin-3beta, nesprin-3alpha, nesprin-3

MMRRC Submission

042827-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5256 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

104896192-104976068 bp(-) (GRCm39)

Type of Mutation

start codon destroyed

DNA Base Change (assembly)

A to T at 104942139 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 1 (M1K)

Ref Sequence

ENSEMBL: ENSMUSP00000093090 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067005] [ENSMUST00000095439] [ENSMUST00000109927]

AlphaFold

Q4FZC9

Predicted Effect

probably benign
Transcript: ENSMUST00000067005

SMART Domains

Protein: ENSMUSP00000065771
Gene: ENSMUSG00000054150

Domain	Start	End	E-Value	Type
Blast:SPEC	29	127	8e-24	BLAST
SPEC	136	237	1.01e-1	SMART
Blast:SPEC	252	446	9e-55	BLAST
low complexity region	447	459	N/A	INTRINSIC
low complexity region	495	514	N/A	INTRINSIC
SPEC	563	664	1.74e-1	SMART
Blast:SPEC	722	818	1e-12	BLAST
KASH	832	888	7.52e-24	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000095439
AA Change: M1K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000093090
Gene: ENSMUSG00000054150
AA Change: M1K

Domain	Start	End	E-Value	Type
SPEC	7	109	1.22e-1	SMART
SPEC	223	324	1.01e-1	SMART
Blast:SPEC	339	533	2e-54	BLAST
low complexity region	534	546	N/A	INTRINSIC
low complexity region	582	601	N/A	INTRINSIC
SPEC	650	751	1.74e-1	SMART
Blast:SPEC	809	905	1e-12	BLAST
KASH	919	975	7.52e-24	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109927

SMART Domains

Protein: ENSMUSP00000105553
Gene: ENSMUSG00000054150

Domain	Start	End	E-Value	Type
Blast:SPEC	29	127	8e-24	BLAST
SPEC	136	237	1.01e-1	SMART
Blast:SPEC	252	446	9e-55	BLAST
low complexity region	447	459	N/A	INTRINSIC
low complexity region	495	514	N/A	INTRINSIC
SPEC	563	664	1.74e-1	SMART
Blast:SPEC	722	818	1e-12	BLAST
KASH	832	888	7.52e-24	SMART

Meta Mutation Damage Score

0.9376

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.8%

Validation Efficiency

97% (95/98)

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730015C16Rik	C	A	4: 108,705,262 (GRCm39)		probably benign	Het
Actr1b	T	C	1: 36,739,173 (GRCm39)	H372R	probably benign	Het
Ampd2	C	A	3: 107,986,865 (GRCm39)		probably benign	Het
Anapc4	A	G	5: 53,020,936 (GRCm39)	S612G	probably benign	Het
Arhgef7	T	C	8: 11,850,811 (GRCm39)	L141P	probably damaging	Het
Atl1	A	G	12: 70,006,107 (GRCm39)	D471G	probably damaging	Het
Atrn	A	G	2: 130,787,939 (GRCm39)	D247G	probably benign	Het
Bag1	T	A	4: 40,948,022 (GRCm39)	R61W	probably damaging	Het
Card10	C	T	15: 78,662,451 (GRCm39)	R898H	probably damaging	Het
Cct6b	G	A	11: 82,655,046 (GRCm39)	A3V	probably damaging	Het
Cfap54	A	T	10: 92,770,953 (GRCm39)	L2097*	probably null	Het
Cfap54	T	C	10: 92,880,885 (GRCm39)		probably null	Het
Chd5	T	C	4: 152,456,554 (GRCm39)	F964L	probably benign	Het
Cog5	A	G	12: 31,936,204 (GRCm39)	T584A	probably benign	Het
Cpa2	T	A	6: 30,547,196 (GRCm39)	N157K	probably damaging	Het
Cpeb1	A	T	7: 81,001,587 (GRCm39)	M440K	probably damaging	Het
Cracr2a	G	A	6: 127,580,992 (GRCm39)	C56Y	probably damaging	Het
Ddb2	A	C	2: 91,067,073 (GRCm39)	L30R	probably damaging	Het
Dlk1	T	A	12: 109,425,697 (GRCm39)	I190N	probably damaging	Het
Dnaaf4	T	C	9: 72,879,362 (GRCm39)		probably null	Het
Dnajc13	T	A	9: 104,080,528 (GRCm39)	Y851F	possibly damaging	Het
Dop1a	T	A	9: 86,397,381 (GRCm39)	L895Q	probably damaging	Het
F7	G	A	8: 13,080,763 (GRCm39)	C122Y	probably damaging	Het
Frrs1	T	C	3: 116,696,749 (GRCm39)	V573A	possibly damaging	Het
Galnt2l	T	C	8: 122,997,175 (GRCm39)		probably benign	Het
Gm17541	A	T	12: 4,739,672 (GRCm39)		probably benign	Het
Gm5519	A	T	19: 33,800,576 (GRCm39)	H90L	probably damaging	Het
Gm5526	T	A	1: 45,896,569 (GRCm39)		noncoding transcript	Het
Gm5709	A	T	3: 59,509,971 (GRCm39)		noncoding transcript	Het
Golga4	T	A	9: 118,385,569 (GRCm39)	V869D	possibly damaging	Het
Grm7	A	T	6: 111,335,182 (GRCm39)	Q531L	probably benign	Het
Hnrnpu	C	A	1: 178,163,458 (GRCm39)	C265F	unknown	Het
Hoxd3	G	A	2: 74,577,211 (GRCm39)	V364I	possibly damaging	Het
Hspb8	T	C	5: 116,547,532 (GRCm39)	D150G	probably damaging	Het
Hydin	C	A	8: 111,313,855 (GRCm39)	N4244K	possibly damaging	Het
Ik	A	G	18: 36,881,926 (GRCm39)	D136G	probably benign	Het
Il11ra1	T	C	4: 41,767,932 (GRCm39)		probably benign	Het
Jph1	T	C	1: 17,161,622 (GRCm39)	I347V	probably benign	Het
Klk1	T	A	7: 43,870,985 (GRCm39)		probably benign	Het
Lmcd1	T	A	6: 112,265,087 (GRCm39)		probably benign	Het
Lnx1	C	T	5: 74,846,315 (GRCm39)	C45Y	probably damaging	Het
Macc1	T	A	12: 119,410,264 (GRCm39)	M344K	possibly damaging	Het
Madcam1	A	G	10: 79,500,779 (GRCm39)	E32G	possibly damaging	Het
Mat2a	T	C	6: 72,411,316 (GRCm39)	D383G	probably benign	Het
Mpst	T	A	15: 78,297,849 (GRCm39)	I289N	probably damaging	Het
Myh6	C	T	14: 55,190,118 (GRCm39)	R1055Q	probably damaging	Het
Myh7	T	C	14: 55,216,965 (GRCm39)	K1131E	probably damaging	Het
Ndrg3	A	T	2: 156,773,125 (GRCm39)		probably benign	Het
Nebl	A	G	2: 17,438,786 (GRCm39)	S209P	probably benign	Het
Nid2	A	G	14: 19,818,276 (GRCm39)		probably null	Het
Nup188	A	T	2: 30,220,761 (GRCm39)	S945C	probably damaging	Het
Or1j21	A	G	2: 36,683,685 (GRCm39)	M146V	probably benign	Het
Or5g23	C	T	2: 85,438,817 (GRCm39)	V146I	probably benign	Het
Or8c11	A	G	9: 38,289,213 (GRCm39)	N12S	probably benign	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Patl2	A	G	2: 121,959,368 (GRCm39)	L32P	probably damaging	Het
Pcdh20	T	A	14: 88,705,813 (GRCm39)	M496L	probably benign	Het
Pdzd2	A	G	15: 12,373,028 (GRCm39)	V2369A	possibly damaging	Het
Pfn2	A	G	3: 57,754,812 (GRCm39)	V31A	probably damaging	Het
Plxna4	T	C	6: 32,228,007 (GRCm39)	N533S	probably benign	Het
Plxnb1	T	C	9: 108,943,661 (GRCm39)	F1916S	probably damaging	Het
Ppp4r3b	T	C	11: 29,138,293 (GRCm39)	F214L	probably benign	Het
Prox1	T	C	1: 189,893,638 (GRCm39)	D269G	probably benign	Het
Rapgef4	T	C	2: 71,864,378 (GRCm39)	F71S	probably damaging	Het
Rft1	A	G	14: 30,383,243 (GRCm39)	I94M	probably benign	Het
S100z	T	C	13: 95,615,127 (GRCm39)	I13V	probably damaging	Het
Serhl	T	A	15: 82,986,835 (GRCm39)	V117E	probably damaging	Het
Shroom1	G	A	11: 53,356,334 (GRCm39)	R336Q	probably benign	Het
Sik3	A	T	9: 46,123,552 (GRCm39)	Q1067L	probably damaging	Het
Slc22a30	G	A	19: 8,321,757 (GRCm39)	Q436*	probably null	Het
Slc28a1	G	A	7: 80,771,869 (GRCm39)	V118M	probably damaging	Het
Slco1a6	T	A	6: 142,078,427 (GRCm39)	I153F	probably benign	Het
Ss18l1	T	C	2: 179,703,735 (GRCm39)	Y323H	unknown	Het
Susd4	G	T	1: 182,719,824 (GRCm39)	A480S	possibly damaging	Het
Synpo2l	A	T	14: 20,711,082 (GRCm39)	S513T	probably benign	Het
Tat	A	T	8: 110,724,966 (GRCm39)	N388I	probably benign	Het
Tbc1d1	A	G	5: 64,439,352 (GRCm39)	Y619C	probably damaging	Het
Tbk1	G	A	10: 121,406,590 (GRCm39)	T216M	probably damaging	Het
Tns1	C	T	1: 74,034,585 (GRCm39)		probably benign	Het
Trbv5	T	C	6: 41,039,318 (GRCm39)	V9A	possibly damaging	Het
Trpm5	A	G	7: 142,636,040 (GRCm39)	Y575H	probably damaging	Het
Ttn	A	T	2: 76,570,045 (GRCm39)	Y25203*	probably null	Het
Tubb3	C	A	8: 124,148,391 (GRCm39)	D441E	probably benign	Het
Usp33	T	A	3: 152,097,333 (GRCm39)	C850*	probably null	Het
Vdac1	G	A	11: 52,274,905 (GRCm39)		probably null	Het
Vmn1r232	T	C	17: 21,133,846 (GRCm39)	I251M	probably damaging	Het
Vmn2r11	T	G	5: 109,202,658 (GRCm39)	I140L	probably benign	Het
Vmn2r6	A	T	3: 64,464,263 (GRCm39)	N190K	probably benign	Het
Vps51	T	A	19: 6,120,518 (GRCm39)	H465L	probably benign	Het
Zfp318	T	G	17: 46,722,995 (GRCm39)	I1666S	probably benign	Het
Zfp446	C	T	7: 12,713,231 (GRCm39)	R90*	probably null	Het
Zgrf1	T	A	3: 127,396,094 (GRCm39)	F547I	probably damaging	Het

Other mutations in Syne3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01154:Syne3	APN	12	104,924,328 (GRCm39)	missense	probably benign	0.00
IGL01986:Syne3	APN	12	104,934,259 (GRCm39)	missense	probably damaging	1.00
IGL02303:Syne3	APN	12	104,929,553 (GRCm39)	missense	probably damaging	1.00
IGL02469:Syne3	APN	12	104,920,565 (GRCm39)	missense	probably benign	0.08
IGL03127:Syne3	APN	12	104,909,687 (GRCm39)	missense	probably benign	0.02
BB008:Syne3	UTSW	12	104,929,491 (GRCm39)	missense	probably damaging	0.97
BB018:Syne3	UTSW	12	104,929,491 (GRCm39)	missense	probably damaging	0.97
PIT4791001:Syne3	UTSW	12	104,929,438 (GRCm39)	missense	probably benign
R0436:Syne3	UTSW	12	104,913,183 (GRCm39)	missense	possibly damaging	0.95
R0471:Syne3	UTSW	12	104,909,685 (GRCm39)	missense	probably benign	0.00
R0613:Syne3	UTSW	12	104,924,371 (GRCm39)	missense	probably benign
R0662:Syne3	UTSW	12	104,927,769 (GRCm39)	missense	probably benign	0.44
R0707:Syne3	UTSW	12	104,935,619 (GRCm39)	missense	probably damaging	0.98
R1321:Syne3	UTSW	12	104,942,055 (GRCm39)	missense	probably benign	0.14
R1494:Syne3	UTSW	12	104,921,841 (GRCm39)	missense	possibly damaging	0.87
R2035:Syne3	UTSW	12	104,924,386 (GRCm39)	missense	probably benign	0.00
R2147:Syne3	UTSW	12	104,919,357 (GRCm39)	missense	probably damaging	1.00
R2326:Syne3	UTSW	12	104,935,493 (GRCm39)	missense	probably damaging	1.00
R2923:Syne3	UTSW	12	104,934,343 (GRCm39)	missense	probably damaging	1.00
R3710:Syne3	UTSW	12	104,909,697 (GRCm39)	missense	possibly damaging	0.86
R3946:Syne3	UTSW	12	104,924,325 (GRCm39)	missense	probably damaging	1.00
R4542:Syne3	UTSW	12	104,935,503 (GRCm39)	missense	probably benign	0.00
R4544:Syne3	UTSW	12	104,925,728 (GRCm39)	missense	probably damaging	1.00
R5110:Syne3	UTSW	12	104,909,629 (GRCm39)	missense	probably benign	0.10
R5490:Syne3	UTSW	12	104,921,931 (GRCm39)	missense	probably damaging	1.00
R5616:Syne3	UTSW	12	104,921,937 (GRCm39)	missense	probably damaging	1.00
R5730:Syne3	UTSW	12	104,927,713 (GRCm39)	missense	probably benign	0.02
R5941:Syne3	UTSW	12	104,913,251 (GRCm39)	missense	probably benign
R6208:Syne3	UTSW	12	104,909,622 (GRCm39)	missense	probably benign	0.12
R6456:Syne3	UTSW	12	104,906,963 (GRCm39)	missense	possibly damaging	0.87
R6566:Syne3	UTSW	12	104,912,966 (GRCm39)	missense	probably benign	0.00
R6957:Syne3	UTSW	12	104,920,561 (GRCm39)	missense	probably damaging	1.00
R7251:Syne3	UTSW	12	104,927,830 (GRCm39)	frame shift	probably null
R7388:Syne3	UTSW	12	104,934,167 (GRCm39)	missense	probably damaging	1.00
R7591:Syne3	UTSW	12	104,906,863 (GRCm39)	critical splice donor site	probably null
R7614:Syne3	UTSW	12	104,912,901 (GRCm39)	missense	not run
R7740:Syne3	UTSW	12	104,920,546 (GRCm39)	missense	probably benign	0.01
R7763:Syne3	UTSW	12	104,963,754 (GRCm39)	start gained	probably benign
R7931:Syne3	UTSW	12	104,929,491 (GRCm39)	missense	probably damaging	0.97
R8973:Syne3	UTSW	12	104,925,654 (GRCm39)	critical splice donor site	probably null
R9031:Syne3	UTSW	12	104,905,871 (GRCm39)	missense	probably benign	0.45
R9263:Syne3	UTSW	12	104,934,415 (GRCm39)	missense	probably damaging	1.00
R9579:Syne3	UTSW	12	104,942,107 (GRCm39)	missense	probably damaging	0.96
R9665:Syne3	UTSW	12	104,924,247 (GRCm39)	missense	probably benign	0.01
R9668:Syne3	UTSW	12	104,898,468 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCAGAACTTCAGCCTCAGC -3'
(R):5'- GCCTACTGTTCCCATAGCAC -3'

Sequencing Primer
(F):5'- GCCTCAGCTCCAGACCAG -3'
(R):5'- CATTTCTAGCTCTGGACACTTAAG -3'

Posted On

2016-07-06