Mutagenetix > Incidental Mutation

Incidental Mutation 'R5325:Syne4'

421888

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

042908-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.112) question?

Stock #

R5325 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30014268-30018471 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30018401 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 381 (Y381F)

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: Y381F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000055874
Gene: ENSMUSG00000019737
AA Change: Y381F

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: ENSMUST00000175902

Predicted Effect

unknown
Transcript: ENSMUST00000176304
AA Change: Y298F

SMART Domains

Protein: ENSMUSP00000135637
Gene: ENSMUSG00000019737
AA Change: Y298F

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: ENSMUST00000176536

Predicted Effect

unknown
Transcript: ENSMUST00000176571
AA Change: Y71F

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176253

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176984

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175672

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176965

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176006

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176071

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

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

0.4193

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.6%
20x: 96.0%

Validation Efficiency

98% (55/56)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ace3	T	A	11: 105,896,079 (GRCm39)	M675K	probably benign	Het
Ccdc186	A	T	19: 56,801,613 (GRCm39)	I168N	probably damaging	Het
Ccnb1	C	G	13: 100,918,283 (GRCm39)	Q121H	possibly damaging	Het
Cep83	A	G	10: 94,573,768 (GRCm39)	E219G	probably damaging	Het
Ctsj	T	C	13: 61,151,839 (GRCm39)	T73A	possibly damaging	Het
Ddr2	T	A	1: 169,829,406 (GRCm39)	T283S	probably benign	Het
Ehbp1	T	A	11: 22,045,370 (GRCm39)	D768V	possibly damaging	Het
Evpl	T	C	11: 116,112,191 (GRCm39)	D1833G	probably damaging	Het
Exoc1	A	G	5: 76,685,549 (GRCm39)	N87S	probably benign	Het
Fam98b	A	C	2: 117,101,132 (GRCm39)	I315L	possibly damaging	Het
Fancg	A	G	4: 43,006,564 (GRCm39)	V330A	probably damaging	Het
Fbxo30	G	A	10: 11,166,846 (GRCm39)	V523I	possibly damaging	Het
Fbxw27	A	G	9: 109,599,161 (GRCm39)	C419R	probably damaging	Het
Flt3	C	A	5: 147,312,459 (GRCm39)	V161L	probably benign	Het
Fndc7	G	A	3: 108,790,765 (GRCm39)	T87I	probably damaging	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Gm6457	A	T	18: 14,703,498 (GRCm39)		noncoding transcript	Het
Gpr63	T	C	4: 25,007,294 (GRCm39)	V6A	probably benign	Het
Grhl3	T	A	4: 135,286,415 (GRCm39)	K89*	probably null	Het
H2-M10.2	C	A	17: 36,596,471 (GRCm39)	V125L	probably benign	Het
Hrh4	C	T	18: 13,155,054 (GRCm39)	Q198*	probably null	Het
Lrch4	A	G	5: 137,636,168 (GRCm39)	E373G	probably damaging	Het
Mroh9	C	G	1: 162,888,329 (GRCm39)	G249R	probably damaging	Het
Noa1	A	C	5: 77,452,042 (GRCm39)	D547E	probably damaging	Het
Nr2e1	G	A	10: 42,448,780 (GRCm39)	R153W	probably damaging	Het
Nudt9	A	C	5: 104,198,487 (GRCm39)	M1L	possibly damaging	Het
Odf2	T	A	2: 29,802,583 (GRCm39)	D282E	probably benign	Het
Olfr908	A	T	9: 38,427,454 (GRCm39)	N42I	probably damaging	Het
Or13a25	C	A	7: 140,247,705 (GRCm39)	H168Q	probably benign	Het
Or6ae1	T	A	7: 139,742,026 (GRCm39)	Y279F	probably damaging	Het
Osbpl5	C	G	7: 143,245,665 (GRCm39)	A816P	probably damaging	Het
Pan2	T	C	10: 128,153,503 (GRCm39)	I924T	possibly damaging	Het
Ppat	A	G	5: 77,076,269 (GRCm39)		probably benign	Het
Rad50	T	G	11: 53,583,690 (GRCm39)	I364L	probably benign	Het
Rnf7l	A	G	10: 63,257,458 (GRCm39)	S21P	probably benign	Het
Robo2	A	G	16: 73,770,673 (GRCm39)	I484T	possibly damaging	Het
Ryr2	A	T	13: 11,705,249 (GRCm39)	M2839K	probably damaging	Het
Sin3b	A	G	8: 73,477,154 (GRCm39)	D807G	probably damaging	Het
Sirpb1a	G	A	3: 15,476,503 (GRCm39)	T98I	possibly damaging	Het
Smim17	G	A	7: 6,432,321 (GRCm39)	V88M	probably damaging	Het
Spib	T	C	7: 44,177,505 (GRCm39)	T229A	probably damaging	Het
St14	A	T	9: 31,008,274 (GRCm39)		probably null	Het
Sytl1	T	C	4: 132,988,382 (GRCm39)		probably benign	Het
Tnpo3	A	C	6: 29,602,012 (GRCm39)		probably benign	Het
Trim12a	T	A	7: 103,953,413 (GRCm39)	I233F	probably damaging	Het
Tspan1	T	A	4: 116,021,536 (GRCm39)	N82Y	probably damaging	Het
Vmn1r60	T	A	7: 5,547,201 (GRCm39)	M300L	probably benign	Het
Wdr17	G	A	8: 55,112,716 (GRCm39)	A788V	possibly damaging	Het
Wwtr1	A	T	3: 57,482,658 (GRCm39)	V63E	probably benign	Het
Ylpm1	A	G	12: 85,060,735 (GRCm39)		probably benign	Het
Zfp956	T	C	6: 47,928,012 (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
R0089:Syne4	UTSW	7	30,018,344 (GRCm39)	missense	probably damaging	0.99
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
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'- GGCCCACCCTTGGTTTTAATAC -3'
(R):5'- TTTGTGTCACAATTTGGGGACC -3'

Sequencing Primer
(F):5'- AATACCGTGTCTCTTCTCAGGG -3'
(R):5'- GGGACCACCACTAAGACAGC -3'

Posted On

2016-08-04