Mutagenetix > Incidental Mutation

Incidental Mutation 'R7740:Syne3'

596511

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

045796-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7740 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

104896192-104976068 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 104920546 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 550 (K550R)

Ref Sequence

ENSEMBL: ENSMUSP00000093090 (fasta)

Gene Model

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

AlphaFold

Q4FZC9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000067005
AA Change: K463R

PolyPhen 2 Score 0.539 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000065771
Gene: ENSMUSG00000054150
AA Change: K463R

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 benign
Transcript: ENSMUST00000095439
AA Change: K550R

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000093090
Gene: ENSMUSG00000054150
AA Change: K550R

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

possibly damaging
Transcript: ENSMUST00000109927
AA Change: K463R

PolyPhen 2 Score 0.539 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000105553
Gene: ENSMUSG00000054150
AA Change: K463R

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

100% (65/65)

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	G	A	5: 109,885,370 (GRCm39)	Q163*	probably null	Het
Anxa6	T	A	11: 54,898,725 (GRCm39)	T150S	probably damaging	Het
Bpifb6	T	A	2: 153,744,929 (GRCm39)	L45Q	probably damaging	Het
Brwd1	T	C	16: 95,828,568 (GRCm39)	D1121G	probably damaging	Het
C1ql3	A	G	2: 13,015,483 (GRCm39)	I59T	possibly damaging	Het
Ccdc80	A	G	16: 44,924,888 (GRCm39)	H674R	possibly damaging	Het
Cdhr1	T	G	14: 36,811,337 (GRCm39)	E258A	probably damaging	Het
Ces2g	T	A	8: 105,692,962 (GRCm39)	F333L	probably damaging	Het
Chn2	C	T	6: 54,277,156 (GRCm39)	T445I	probably benign	Het
Cpe	T	C	8: 65,050,562 (GRCm39)	D382G	possibly damaging	Het
Crb1	T	A	1: 139,165,428 (GRCm39)	I960L	probably benign	Het
Cyp4a14	A	T	4: 115,350,806 (GRCm39)	V156D	probably damaging	Het
Ddx23	A	T	15: 98,556,315 (GRCm39)	M1K	probably null	Het
Dnajc7	T	C	11: 100,482,387 (GRCm39)	I202V	probably benign	Het
Dsn1	T	A	2: 156,839,636 (GRCm39)	D255V	possibly damaging	Het
Dvl3	A	T	16: 20,346,000 (GRCm39)		probably null	Het
Epm2a	A	G	10: 11,266,684 (GRCm39)	D143G	possibly damaging	Het
Erc1	T	A	6: 119,738,149 (GRCm39)	M565L	probably benign	Het
Fancm	T	C	12: 65,173,321 (GRCm39)	C1878R	possibly damaging	Het
Gapvd1	T	C	2: 34,590,834 (GRCm39)	E946G	probably damaging	Het
Gm9195	C	T	14: 72,678,113 (GRCm39)	R2352K	possibly damaging	Het
Greb1	C	A	12: 16,790,122 (GRCm39)		probably benign	Het
Haus5	G	A	7: 30,362,678 (GRCm39)	A44V	possibly damaging	Het
Herc4	A	G	10: 63,105,457 (GRCm39)	Y146C	probably benign	Het
Herc6	T	G	6: 57,636,802 (GRCm39)		probably null	Het
Hivep2	G	T	10: 14,003,414 (GRCm39)	G4V	probably damaging	Het
Hsdl2	G	T	4: 59,612,724 (GRCm39)	G425V	probably damaging	Het
Igkv1-110	C	T	6: 68,247,974 (GRCm39)	L28F	probably benign	Het
Il21r	T	A	7: 125,231,727 (GRCm39)	L385Q	possibly damaging	Het
Krtap5-1	ACAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAG	ACAGGGCTTGCAGCAGCTGGACTGACAGCAGCAGGGCTTGCAGCAGCTGGACTGACAGCAG	7: 141,850,333 (GRCm39)		probably benign	Het
Krtap5-2	C	T	7: 141,728,699 (GRCm39)	C149Y	unknown	Het
Lingo2	T	A	4: 35,709,248 (GRCm39)	N244I	probably damaging	Het
Lrrk2	C	T	15: 91,651,527 (GRCm39)	R1728C	probably damaging	Het
Macf1	A	G	4: 123,578,096 (GRCm39)		probably benign	Het
Malrd1	G	A	2: 15,619,026 (GRCm39)	V297I	not run	Het
Mars1	T	A	10: 127,136,444 (GRCm39)	E460D	probably benign	Het
Nr1i3	A	G	1: 171,044,396 (GRCm39)	I174V	probably benign	Het
Odf2	C	T	2: 29,820,636 (GRCm39)	T814M	probably damaging	Het
Or10q1	T	C	19: 13,727,328 (GRCm39)	V286A	probably benign	Het
Or4k1	T	C	14: 50,377,803 (GRCm39)	M98V	probably benign	Het
Or4k52	A	T	2: 111,610,793 (GRCm39)	I43F	possibly damaging	Het
Pcdhga8	T	C	18: 37,860,470 (GRCm39)	S509P	probably benign	Het
Pdzd2	A	G	15: 12,374,102 (GRCm39)	L2011S	probably benign	Het
Pole	T	A	5: 110,478,907 (GRCm39)	S1930T	probably benign	Het
Poteg	T	A	8: 27,952,052 (GRCm39)		probably null	Het
Ptprk	T	A	10: 28,372,920 (GRCm39)	C724S	probably damaging	Het
Rabgap1l	T	C	1: 160,509,673 (GRCm39)	E468G	probably benign	Het
Rbm12b1	G	T	4: 12,145,954 (GRCm39)	R642L	probably benign	Het
Relch	T	C	1: 105,658,986 (GRCm39)	V914A	probably damaging	Het
S1pr4	A	T	10: 81,334,855 (GRCm39)	Y206*	probably null	Het
Sim2	A	G	16: 93,915,819 (GRCm39)	I261V	probably benign	Het
Slc22a12	C	A	19: 6,587,199 (GRCm39)	A448S	probably benign	Het
Slc4a2	A	G	5: 24,636,666 (GRCm39)		probably null	Het
Slc6a7	T	C	18: 61,133,495 (GRCm39)	E567G	possibly damaging	Het
St6gal1	T	C	16: 23,139,785 (GRCm39)		probably benign	Het
Tekt1	T	A	11: 72,250,544 (GRCm39)	T51S	probably benign	Het
Tm9sf4	T	A	2: 153,050,663 (GRCm39)	V640E	probably damaging	Het
Tnfsf8	G	T	4: 63,752,683 (GRCm39)	H127Q	possibly damaging	Het
Tomm20	A	G	8: 127,666,633 (GRCm39)	L80S	probably damaging	Het
Top2a	T	C	11: 98,884,640 (GRCm39)	D1526G	probably benign	Het
Trmt1l	T	C	1: 151,316,639 (GRCm39)	V200A	possibly damaging	Het
Trpa1	A	G	1: 14,982,625 (GRCm39)	V77A	possibly damaging	Het
Vmn2r12	A	T	5: 109,239,615 (GRCm39)	V316D	probably damaging	Het
Vmn2r14	A	T	5: 109,368,324 (GRCm39)	L223M	probably benign	Het
Zfp2	T	C	11: 50,791,605 (GRCm39)	H146R	probably damaging	Het
Zfp52	T	C	17: 21,781,252 (GRCm39)	S367P	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
R5256:Syne3	UTSW	12	104,942,139 (GRCm39)	start codon destroyed	probably null	1.00
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
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'- GATTCCATTGAGACCCACGC -3'
(R):5'- CCTGCACAGACAATGGCTAAAG -3'

Sequencing Primer
(F):5'- ATCCCGGCAGTAATGGACC -3'
(R):5'- TGGCTAAAGTGTGATAAGGGGACAC -3'

Posted On

2019-11-26