Mutagenetix > Incidental Mutation

Incidental Mutation 'R9596:Syne4'

723273

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

Accession Numbers

Essential gene?

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

Stock #

R9596 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

30014268-30018471 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 30014504 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 41 (T41A)

Ref Sequence

ENSEMBL: ENSMUSP00000055874 (fasta)

Gene Model

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

AlphaFold

Q8CII8

Predicted Effect

probably benign
Transcript: ENSMUST00000054594
AA Change: T41A

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

SMART Domains

Protein: ENSMUSP00000055874
Gene: ENSMUSG00000019737
AA Change: T41A

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: 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

probably benign
Transcript: ENSMUST00000137550

Predicted Effect

probably benign
Transcript: ENSMUST00000176304
AA Change: T41A

PolyPhen 2 Score 0.254 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000135637
Gene: ENSMUSG00000019737
AA Change: T41A

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

probably benign
Transcript: ENSMUST00000176504
AA Change: T41A

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000135844
Gene: ENSMUSG00000019737
AA Change: T41A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000176571

Predicted Effect

probably benign
Transcript: ENSMUST00000176789

Predicted Effect

probably benign
Transcript: ENSMUST00000177078
AA Change: T41A

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000135895
Gene: ENSMUSG00000019737
AA Change: T41A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aamp	G	T	1: 74,320,262 (GRCm39)	Q355K	probably benign	Het
Acte1	G	T	7: 143,434,902 (GRCm39)		probably null	Het
AI661453	T	C	17: 47,780,411 (GRCm39)	S188P	unknown	Het
Atp10a	A	G	7: 58,477,553 (GRCm39)	S1251G	probably damaging	Het
Ccr10	A	G	11: 101,065,018 (GRCm39)	F171L	probably benign	Het
Clec10a	A	T	11: 70,059,973 (GRCm39)	D65V	probably damaging	Het
Clybl	A	T	14: 122,548,768 (GRCm39)	I57L	probably benign	Het
Col5a1	G	T	2: 27,819,551 (GRCm39)	E218*	probably null	Het
Diaph1	G	A	18: 38,024,111 (GRCm39)	P576S	unknown	Het
Dsg1c	T	A	18: 20,416,361 (GRCm39)	I754N	probably benign	Het
Fam47e	G	C	5: 92,726,395 (GRCm39)	R111P	probably benign	Het
Fastkd3	G	A	13: 68,735,806 (GRCm39)	V519M	probably damaging	Het
Fhod3	T	A	18: 25,193,392 (GRCm39)	Y634*	probably null	Het
Frem3	G	A	8: 81,341,951 (GRCm39)	V1415I	probably benign	Het
Herc2	G	A	7: 55,834,595 (GRCm39)	S3191N		Het
Kif19a	A	T	11: 114,676,752 (GRCm39)	E527V	probably benign	Het
Lmbr1	C	A	5: 29,440,105 (GRCm39)	G420*	probably null	Het
Map3k9	A	G	12: 81,777,404 (GRCm39)	S526P	probably damaging	Het
Mink1	T	A	11: 70,497,915 (GRCm39)	L506Q	possibly damaging	Het
Mroh9	T	C	1: 162,893,576 (GRCm39)	I200V	probably damaging	Het
Mrps14	T	C	1: 160,027,122 (GRCm39)	V110A	possibly damaging	Het
Mta1	A	G	12: 113,090,470 (GRCm39)	Q209R	probably damaging	Het
Mtss2	G	A	8: 111,458,689 (GRCm39)	S195N		Het
Nlgn1	T	A	3: 25,488,587 (GRCm39)	I583F	probably damaging	Het
Ntng1	T	C	3: 110,042,956 (GRCm39)		probably benign	Het
Or10w1	A	G	19: 13,632,002 (GRCm39)	S70G	probably damaging	Het
Or1p1c	C	T	11: 74,160,289 (GRCm39)	H25Y	probably benign	Het
Or2ag13	A	T	7: 106,313,412 (GRCm39)	Y159N	probably benign	Het
Or5ac25	A	G	16: 59,181,942 (GRCm39)	I213T	possibly damaging	Het
Or6c65	A	G	10: 129,603,988 (GRCm39)	T208A	probably damaging	Het
Pcdha12	A	T	18: 37,154,302 (GRCm39)	L340F	probably benign	Het
Pdk4	T	A	6: 5,491,842 (GRCm39)	M173L	probably benign	Het
Pds5a	A	G	5: 65,772,830 (GRCm39)	S1258P	probably benign	Het
Plcd1	A	T	9: 118,917,183 (GRCm39)	L22Q	probably benign	Het
Prag1	A	G	8: 36,570,113 (GRCm39)	D232G	probably damaging	Het
Rest	C	T	5: 77,423,141 (GRCm39)	T315M	probably damaging	Het
Scrn2	G	A	11: 96,923,907 (GRCm39)	V264M	probably damaging	Het
Sipa1l3	C	A	7: 29,031,691 (GRCm39)	V1513F	probably benign	Het
Skic3	T	C	13: 76,330,968 (GRCm39)	V1466A	possibly damaging	Het
Slc44a1	T	A	4: 53,544,553 (GRCm39)	N421K	probably benign	Het
Smc6	G	T	12: 11,345,045 (GRCm39)	R662I	probably damaging	Het
Spata31e5	C	A	1: 28,815,688 (GRCm39)	M781I	probably benign	Het
Srcap	T	A	7: 127,131,036 (GRCm39)	W751R	probably damaging	Het
Sv2b	A	G	7: 74,767,462 (GRCm39)	F645L	probably damaging	Het
Sycp2	A	G	2: 177,990,212 (GRCm39)		probably null	Het
Tns3	G	A	11: 8,401,142 (GRCm39)	T1052M	possibly damaging	Het
Trap1	A	T	16: 3,871,374 (GRCm39)	I381N	probably damaging	Het
Tshz1	A	G	18: 84,031,904 (GRCm39)	S835P	possibly damaging	Het
Ube3b	T	A	5: 114,527,171 (GRCm39)	W130R	probably damaging	Het
Ubr5	G	A	15: 37,986,213 (GRCm39)	T2207I		Het
Vmn1r43	G	A	6: 89,846,877 (GRCm39)	T203M	probably damaging	Het
Vmn2r11	T	G	5: 109,201,563 (GRCm39)	I314L	possibly damaging	Het
Vmn2r15	T	A	5: 109,440,791 (GRCm39)	I356L	probably benign	Het
Vmn2r31	G	T	7: 7,397,292 (GRCm39)	T322N	probably benign	Het
Vmn2r8	A	T	5: 108,947,196 (GRCm39)	F519I	possibly damaging	Het
Wdr35	T	C	12: 9,036,092 (GRCm39)	F288L	probably benign	Het
Xab2	A	T	8: 3,663,018 (GRCm39)	V521D	probably damaging	Het
Zfp639	T	C	3: 32,574,269 (GRCm39)	F298S	probably damaging	Het
Zfp786	G	A	6: 47,797,406 (GRCm39)	R511*	probably null	Het
Zfp936	T	A	7: 42,839,834 (GRCm39)	C434S	probably damaging	Het
Zranb1	T	C	7: 132,552,146 (GRCm39)	F266L	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
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
Z1088:Syne4	UTSW	7	30,015,761 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GACTTAGGCTGTGAGTCCTG -3'
(R):5'- AGAAAGGTTGATGGGCCACC -3'

Sequencing Primer
(F):5'- CTGTCTAAGAAAGCGGCTGC -3'
(R):5'- TGATGGGCCACCTGTGAG -3'

Posted On

2022-08-09