Mutagenetix > Incidental Mutation

Incidental Mutation 'R6479:Syne4'

516975

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

044611-MU

Accession Numbers

Essential gene?

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

Stock #

R6479 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

30014268-30018471 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to T at 30016340 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Stop codon at position 179 (G179*)

Ref Sequence

ENSEMBL: ENSMUSP00000135895 (fasta)

Gene Model

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

AlphaFold

Q8CII8

Predicted Effect

probably null
Transcript: ENSMUST00000054594
AA Change: G227*

SMART Domains

Protein: ENSMUSP00000055874
Gene: ENSMUSG00000019737
AA Change: G227*

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: ENSMUST00000135319

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135882

Predicted Effect

probably null
Transcript: ENSMUST00000176504
AA Change: G199*

SMART Domains

Protein: ENSMUSP00000135844
Gene: ENSMUSG00000019737
AA Change: G199*

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

noncoding transcript
Transcript: ENSMUST00000175902

Predicted Effect

probably benign
Transcript: ENSMUST00000176304

SMART Domains

Protein: ENSMUSP00000135637
Gene: ENSMUSG00000019737

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: ENSMUST00000175672

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148858

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137870

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176071

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144951

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176253

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: ENSMUST00000176006

Predicted Effect

probably benign
Transcript: ENSMUST00000137550

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143369

Predicted Effect

probably null
Transcript: ENSMUST00000177078
AA Change: G179*

SMART Domains

Protein: ENSMUSP00000135895
Gene: ENSMUSG00000019737
AA Change: G179*

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

Predicted Effect

probably benign
Transcript: ENSMUST00000176571

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177395

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176984

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176536

Predicted Effect

probably benign
Transcript: ENSMUST00000176789

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177257

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176965

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.7%
20x: 92.0%

Validation Efficiency

95% (55/58)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	A	C	8: 25,119,681 (GRCm39)	S533A	probably benign	Het
Akap6	T	G	12: 53,187,952 (GRCm39)	S1789A	probably damaging	Het
Alox15	A	G	11: 70,236,011 (GRCm39)	S519P	probably damaging	Het
Anapc2	A	G	2: 25,175,407 (GRCm39)	K816E	probably benign	Het
Atp6v1a	T	C	16: 43,919,121 (GRCm39)	D488G	probably benign	Het
Banp	A	G	8: 122,718,176 (GRCm39)		probably null	Het
Camsap1	A	G	2: 25,825,874 (GRCm39)	C1367R	possibly damaging	Het
Casz1	C	A	4: 149,021,535 (GRCm39)	H539Q	probably damaging	Het
Ccl5	A	G	11: 83,421,212 (GRCm39)	Y26H	probably benign	Het
Cops3	A	T	11: 59,723,898 (GRCm39)	S86R	probably benign	Het
Cts7	A	G	13: 61,503,455 (GRCm39)	S170P	probably benign	Het
Cxcl15	A	T	5: 90,943,104 (GRCm39)	E35D	possibly damaging	Het
Dennd1b	C	T	1: 138,969,698 (GRCm39)		probably benign	Het
Dicer1	T	C	12: 104,662,982 (GRCm39)	D1533G	probably damaging	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Dock4	A	G	12: 40,878,954 (GRCm39)	E1531G	probably damaging	Het
Erap1	A	G	13: 74,811,612 (GRCm39)		probably null	Het
Fsip2	A	G	2: 82,820,430 (GRCm39)	T5388A	possibly damaging	Het
Gab1	C	A	8: 81,515,226 (GRCm39)	R364L	possibly damaging	Het
Gm10309	A	T	17: 86,812,007 (GRCm39)	M1K	probably null	Het
Gm4884	A	T	7: 40,690,211 (GRCm39)	N36Y	probably damaging	Het
Hmcn1	G	A	1: 150,553,053 (GRCm39)	R2546*	probably null	Het
Hmcn2	A	G	2: 31,315,480 (GRCm39)	D3743G	probably damaging	Het
Hsd3b9	T	A	3: 98,354,157 (GRCm39)	E114V	possibly damaging	Het
Irak2	A	T	6: 113,663,902 (GRCm39)	N423Y	probably damaging	Het
Jarid2	G	A	13: 45,001,765 (GRCm39)	G26D	probably benign	Het
Kif13b	A	G	14: 64,988,974 (GRCm39)	K785R	probably benign	Het
Lamc3	A	T	2: 31,777,413 (GRCm39)	I20F	probably benign	Het
Limk1	G	A	5: 134,690,373 (GRCm39)		probably benign	Het
Lrp4	C	T	2: 91,317,429 (GRCm39)	T851I	probably damaging	Het
Med13	G	A	11: 86,248,353 (GRCm39)		probably benign	Het
Megf10	T	C	18: 57,379,642 (GRCm39)	F273L	possibly damaging	Het
Meltf	T	A	16: 31,700,700 (GRCm39)	D73E	probably damaging	Het
Mroh7	A	G	4: 106,560,385 (GRCm39)	F640L	possibly damaging	Het
Mtor	T	C	4: 148,635,457 (GRCm39)	S2448P	probably benign	Het
Myo3a	T	C	2: 22,467,877 (GRCm39)	V377A	probably benign	Het
Myo5b	T	C	18: 74,750,086 (GRCm39)	V183A	probably damaging	Het
Nedd4l	G	A	18: 65,342,752 (GRCm39)	R755H	probably damaging	Het
Nrde2	T	C	12: 100,110,207 (GRCm39)	T275A	probably benign	Het
Or52n4	A	G	7: 104,294,333 (GRCm39)	I80T	probably benign	Het
Osgepl1	T	C	1: 53,360,702 (GRCm39)	V381A	probably benign	Het
Pcdha1	C	T	18: 37,064,509 (GRCm39)	T391I	probably benign	Het
Pdp1	T	C	4: 11,961,327 (GRCm39)	N328S	probably damaging	Het
Pepd	A	G	7: 34,740,147 (GRCm39)	E340G	probably benign	Het
Plch1	T	C	3: 63,651,931 (GRCm39)	T387A	probably benign	Het
Plxnb1	C	A	9: 108,940,733 (GRCm39)	T1536K	possibly damaging	Het
Rbp7	T	C	4: 149,534,347 (GRCm39)	T130A	probably benign	Het
Rhot2	A	T	17: 26,060,054 (GRCm39)	V309E	probably benign	Het
Slc37a1	A	G	17: 31,557,964 (GRCm39)	I421M	possibly damaging	Het
Slit2	T	A	5: 48,389,331 (GRCm39)	L585H	probably damaging	Het
Spint4	C	A	2: 164,542,764 (GRCm39)	A119D	probably benign	Het
Strip2	G	T	6: 29,944,496 (GRCm39)		probably null	Het
Stxbp4	T	C	11: 90,510,013 (GRCm39)	Y59C	probably damaging	Het
Syne1	G	A	10: 5,181,679 (GRCm39)	Q4219*	probably null	Het
Syne1	A	T	10: 5,406,826 (GRCm39)	I37N	probably damaging	Het
Tead1	T	C	7: 112,460,672 (GRCm39)	V192A	probably benign	Het
Trim37	G	T	11: 87,107,313 (GRCm39)	E317*	probably null	Het
Wdfy3	A	C	5: 102,061,045 (GRCm39)	Y1390D	probably damaging	Het
Wdr81	A	G	11: 75,342,931 (GRCm39)	F779L	possibly damaging	Het
Zfp1002	C	T	2: 150,096,511 (GRCm39)	G306D	probably damaging	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
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'- CCAGTTGATCAGCTATAGCCTG -3'
(R):5'- TAGAAAGGTACCTTGTGGGGCC -3'

Sequencing Primer
(F):5'- GATCAGCTATAGCCTGGTATGACC -3'
(R):5'- CAGCCAAGTAGGGAGCCTTTG -3'

Posted On

2018-05-21