Mutagenetix > Incidental Mutation

Incidental Mutation 'R0089:Syne4'

60594

Institutional Source

Beutler Lab

Gene Symbol

Syne4

Ensembl Gene

ENSMUSG00000019737

Gene Name

spectrin repeat containing, nuclear envelope family member 4

Synonyms

0610012K07Rik, AI428936, nesprin-4

MMRRC Submission

038376-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.109) question?

Stock #

R0089 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30014268-30018471 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 30018344 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Glutamic Acid at position 362 (G362E)

Ref Sequence

ENSEMBL: ENSMUSP00000055874 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000054594] [ENSMUST00000060834] [ENSMUST00000098585] [ENSMUST00000098586] [ENSMUST00000136887] [ENSMUST00000176304] [ENSMUST00000176504] [ENSMUST00000176789] [ENSMUST00000137550] [ENSMUST00000177078]

AlphaFold

Q8CII8

Predicted Effect

probably damaging
Transcript: ENSMUST00000054594
AA Change: G362E

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000055874
Gene: ENSMUSG00000019737
AA Change: G362E

Domain	Start	End	E-Value	Type
Blast:SPEC	96	198	2e-34	BLAST
low complexity region	222	234	N/A	INTRINSIC
low complexity region	290	315	N/A	INTRINSIC
KASH	335	388	2.85e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000060834

SMART Domains

Protein: ENSMUSP00000051515
Gene: ENSMUSG00000042831

Domain	Start	End	E-Value	Type
Pfam:2OG-FeII_Oxy_2	23	224	3.5e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000098585

SMART Domains

Protein: ENSMUSP00000096184
Gene: ENSMUSG00000074210

Domain	Start	End	E-Value	Type
low complexity region	74	95	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000098586

SMART Domains

Protein: ENSMUSP00000096185
Gene: ENSMUSG00000074211

Domain	Start	End	E-Value	Type
Pfam:Complex1_LYR	9	63	2.1e-16	PFAM
Pfam:Complex1_LYR_1	9	65	5.9e-14	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132193

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135882

Predicted Effect

probably benign
Transcript: ENSMUST00000136887

SMART Domains

Protein: ENSMUSP00000121953
Gene: ENSMUSG00000042831

Domain	Start	End	E-Value	Type
Pfam:2OG-FeII_Oxy_2	3	210	2.1e-16	PFAM
Pfam:2OG-FeII_Oxy	82	213	1.2e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175902

Predicted Effect

possibly damaging
Transcript: ENSMUST00000176304
AA Change: G279E

PolyPhen 2 Score 0.574 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135637
Gene: ENSMUSG00000019737
AA Change: G279E

Domain	Start	End	E-Value	Type
Blast:SPEC	96	196	3e-34	BLAST
low complexity region	197	232	N/A	INTRINSIC
KASH	252	305	2.85e-15	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176965

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176071

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176253

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176984

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175672

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176006

Predicted Effect

probably benign
Transcript: ENSMUST00000176504

SMART Domains

Protein: ENSMUSP00000135844
Gene: ENSMUSG00000019737

Domain	Start	End	E-Value	Type
Blast:SPEC	92	170	2e-33	BLAST
low complexity region	194	206	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176232

Predicted Effect

probably benign
Transcript: ENSMUST00000176789

Predicted Effect

probably benign
Transcript: ENSMUST00000137550

Predicted Effect

probably benign
Transcript: ENSMUST00000176571

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177395

Predicted Effect

probably benign
Transcript: ENSMUST00000177078

SMART Domains

Protein: ENSMUSP00000135895
Gene: ENSMUSG00000019737

Domain	Start	End	E-Value	Type
Blast:SPEC	88	150	4e-24	BLAST
low complexity region	174	186	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177257

Meta Mutation Damage Score

0.3470

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 95.6%
20x: 90.5%

Validation Efficiency

98% (82/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the nesprin family of genes, that encode KASH (Klarsicht, Anc-1, Syne Homology) domain-containing proteins. In addition to the KASH domain, this protein also contains a coiled-coil and leucine zipper region, a spectrin repeat, and a kinesin-1 binding region. This protein localizes to the outer nuclear membrane, and is part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. LINC complexes are formed by SUN (Sad1, UNC-84)-KASH pairs, and are thought to mechanically couple nuclear components to the cytoskeleton. Mutations in this gene have been associated with progressive high-frequency hearing loss. The absence of this protein in mice also caused hearing loss, and changes in hair cell morphology in the ears. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit hearing loss associated with outer hair cell degeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4fm2	T	A	4: 144,282,303 (GRCm39)	H163L	probably benign	Het
Abca13	T	A	11: 9,242,886 (GRCm39)	V1583E	possibly damaging	Het
Ablim1	G	T	19: 57,031,463 (GRCm39)	S654Y	probably damaging	Het
Acbd4	T	C	11: 102,994,819 (GRCm39)	F59S	probably damaging	Het
Acot1	T	C	12: 84,063,708 (GRCm39)	I272T	probably damaging	Het
Ankhd1	A	G	18: 36,773,409 (GRCm39)	D1402G	probably damaging	Het
Birc6	T	A	17: 74,945,371 (GRCm39)	F2800I	possibly damaging	Het
Brd1	T	C	15: 88,585,401 (GRCm39)	E811G	probably benign	Het
Catspere2	C	T	1: 177,874,555 (GRCm39)	P141S	unknown	Het
Ccdc106	A	G	7: 5,059,220 (GRCm39)		probably null	Het
Ccdc81	G	T	7: 89,542,324 (GRCm39)	A184E	possibly damaging	Het
Cenpt	T	C	8: 106,573,000 (GRCm39)	T364A	probably benign	Het
Crybg2	T	C	4: 133,808,505 (GRCm39)	S1060P	probably damaging	Het
Dnttip2	A	G	3: 122,069,111 (GRCm39)	T109A	possibly damaging	Het
Dpy19l2	A	G	9: 24,607,089 (GRCm39)	L124P	probably benign	Het
Eif1ad19	A	T	12: 87,740,283 (GRCm39)	I92N	probably damaging	Het
Fat3	T	C	9: 15,849,501 (GRCm39)	D3967G	probably benign	Het
Fbxo21	T	A	5: 118,146,208 (GRCm39)	F610L	probably benign	Het
Fmo9	T	C	1: 166,494,878 (GRCm39)	D341G	probably benign	Het
Frem3	A	T	8: 81,342,507 (GRCm39)	H1600L	possibly damaging	Het
Fry	A	T	5: 150,263,892 (GRCm39)	K133N	possibly damaging	Het
Gm10647	A	G	9: 66,705,612 (GRCm39)		probably benign	Het
Gmps	T	C	3: 63,906,119 (GRCm39)	F472S	probably benign	Het
Grb10	T	C	11: 11,884,192 (GRCm39)		probably benign	Het
Grm6	G	A	11: 50,750,792 (GRCm39)	G652S	probably damaging	Het
Heca	G	T	10: 17,783,848 (GRCm39)	D468E	probably damaging	Het
Heg1	C	T	16: 33,583,985 (GRCm39)	S1033L	probably damaging	Het
Hepacam2	A	G	6: 3,487,094 (GRCm39)	S12P	probably damaging	Het
Impdh1	G	T	6: 29,206,325 (GRCm39)	H195N	probably benign	Het
Ipo7	T	C	7: 109,649,972 (GRCm39)		probably benign	Het
Itpr2	C	T	6: 146,251,520 (GRCm39)		probably null	Het
Kcnh6	G	A	11: 105,899,848 (GRCm39)	C39Y	probably benign	Het
Kif26a	T	C	12: 112,143,837 (GRCm39)	S1364P	probably damaging	Het
Lins1	T	A	7: 66,361,796 (GRCm39)		probably benign	Het
Lrpap1	C	T	5: 35,252,232 (GRCm39)	V328M	possibly damaging	Het
Lyn	T	G	4: 3,748,768 (GRCm39)	L249V	probably benign	Het
Mpp7	A	G	18: 7,439,555 (GRCm39)		probably benign	Het
Mtmr9	A	G	14: 63,765,696 (GRCm39)	F400L	possibly damaging	Het
Mto1	G	A	9: 78,381,154 (GRCm39)	S666N	probably benign	Het
Nanos3	C	T	8: 84,902,763 (GRCm39)	R133Q	probably damaging	Het
Nsg1	T	C	5: 38,312,974 (GRCm39)	E75G	probably benign	Het
Nsun4	A	G	4: 115,892,970 (GRCm39)	M283T	probably benign	Het
Obscn	A	G	11: 58,890,888 (GRCm39)	S7215P	unknown	Het
Or11j4	T	C	14: 50,630,321 (GRCm39)	I36T	probably benign	Het
Or13a20	T	C	7: 140,232,224 (GRCm39)	S111P	probably damaging	Het
Or1j12	G	A	2: 36,343,107 (GRCm39)	R170K	probably benign	Het
Or2y13	G	A	11: 49,415,033 (GRCm39)	S161N	possibly damaging	Het
Or52e4	T	A	7: 104,706,297 (GRCm39)	Y281*	probably null	Het
Or5al1	A	C	2: 85,989,918 (GRCm39)	S265R	possibly damaging	Het
Or9m1b	T	C	2: 87,836,331 (GRCm39)	I264V	probably damaging	Het
Per1	T	C	11: 68,994,869 (GRCm39)	F563S	probably benign	Het
Pik3c3	T	A	18: 30,436,131 (GRCm39)		probably benign	Het
Pitrm1	A	T	13: 6,605,675 (GRCm39)	K207N	probably damaging	Het
Prdm10	C	T	9: 31,227,526 (GRCm39)	R44C	probably damaging	Het
Rab40c	A	T	17: 26,104,122 (GRCm39)	I90N	probably damaging	Het
Rbl1	A	G	2: 157,041,334 (GRCm39)		probably null	Het
Rnf17	G	A	14: 56,751,563 (GRCm39)	G1467E	probably damaging	Het
Rpgrip1	A	G	14: 52,386,841 (GRCm39)		probably benign	Het
Sall1	A	T	8: 89,756,896 (GRCm39)	N1069K	probably benign	Het
Scap	T	C	9: 110,201,290 (GRCm39)	I93T	possibly damaging	Het
Sez6	T	C	11: 77,865,170 (GRCm39)		probably benign	Het
Slc22a30	A	T	19: 8,347,561 (GRCm39)	S280T	probably benign	Het
Slc26a5	A	C	5: 22,016,342 (GRCm39)		probably null	Het
St18	T	C	1: 6,919,172 (GRCm39)	V901A	probably benign	Het
Syne2	T	C	12: 76,010,650 (GRCm39)	L2519P	probably damaging	Het
Tmem51	T	C	4: 141,759,236 (GRCm39)	T171A	probably benign	Het
Tns4	A	T	11: 98,966,024 (GRCm39)	I453N	probably damaging	Het
Trank1	A	T	9: 111,221,978 (GRCm39)	H2905L	probably benign	Het
Trim13	C	T	14: 61,842,166 (GRCm39)	T61I	possibly damaging	Het
Trim75	T	C	8: 65,435,580 (GRCm39)	Q290R	possibly damaging	Het
Ttn	C	A	2: 76,559,544 (GRCm39)	R29619L	probably damaging	Het
Ugt2b38	T	A	5: 87,568,417 (GRCm39)	M293L	probably benign	Het
Vmn1r22	T	A	6: 57,877,513 (GRCm39)	N155Y	probably benign	Het
Vmn2r18	T	C	5: 151,508,269 (GRCm39)	Y285C	probably benign	Het
Vmn2r84	C	T	10: 130,222,588 (GRCm39)		probably benign	Het
Vwde	A	C	6: 13,220,004 (GRCm39)	L49R	probably damaging	Het
Yipf2	T	A	9: 21,503,262 (GRCm39)	E68D	possibly damaging	Het
Zfand5	C	A	19: 21,257,122 (GRCm39)		probably benign	Het

Other mutations in Syne4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02237:Syne4	APN	7	30,015,988 (GRCm39)	splice site	probably null
IGL02386:Syne4	APN	7	30,015,659 (GRCm39)	missense	possibly damaging	0.91
R0091:Syne4	UTSW	7	30,018,344 (GRCm39)	missense	probably damaging	0.99
R0448:Syne4	UTSW	7	30,014,345 (GRCm39)	start gained	probably benign
R0555:Syne4	UTSW	7	30,016,169 (GRCm39)	missense	probably damaging	0.99
R1205:Syne4	UTSW	7	30,014,761 (GRCm39)	missense	probably damaging	0.96
R1862:Syne4	UTSW	7	30,016,308 (GRCm39)	missense	probably benign	0.06
R1863:Syne4	UTSW	7	30,016,308 (GRCm39)	missense	probably benign	0.06
R4776:Syne4	UTSW	7	30,016,258 (GRCm39)	splice site	probably benign
R5325:Syne4	UTSW	7	30,018,401 (GRCm39)	missense	probably damaging	1.00
R6145:Syne4	UTSW	7	30,015,988 (GRCm39)	splice site	probably null
R6479:Syne4	UTSW	7	30,016,340 (GRCm39)	nonsense	probably null
R7823:Syne4	UTSW	7	30,018,280 (GRCm39)	missense	probably benign	0.09
R9013:Syne4	UTSW	7	30,017,418 (GRCm39)	missense	probably damaging	1.00
R9541:Syne4	UTSW	7	30,016,343 (GRCm39)	missense	probably benign	0.02
R9596:Syne4	UTSW	7	30,014,504 (GRCm39)	missense	probably benign	0.01
Z1088:Syne4	UTSW	7	30,015,761 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TCTGCCTGATGCAATGCTGGAAG -3'
(R):5'- TGCCCTCAAGGCAAAGGAATACAAG -3'

Sequencing Primer
(F):5'- CAATGCTGGAAGTGGATCGC -3'
(R):5'- AGGAGCTGTCAGAACACAC -3'

Posted On

2013-07-24