Mutagenetix > Incidental Mutations

Incidental Mutation 'R6160:Synj2'

489838

Institutional Source

Beutler Lab

Gene Symbol

Synj2

Ensembl Gene

ENSMUSG00000023805

Gene Name

synaptojanin 2

Synonyms

SJ2

MMRRC Submission

044307-MU

Accession Numbers

Genbank: NM_001113353.1, NM_001113352.1, NM_011523.2, NM_001113351.1

Is this an essential gene?

Probably non essential (E-score: 0.122) question?

Stock #

R6160 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

5941280-6044290 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 6008061 bp

Zygosity

Heterozygous

Amino Acid Change

Histidine to Asparagine at position 275 (H275N)

Ref Sequence

ENSEMBL: ENSMUSP00000111456 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000061091] [ENSMUST00000080283] [ENSMUST00000115784] [ENSMUST00000115785] [ENSMUST00000115786] [ENSMUST00000115787] [ENSMUST00000115788] [ENSMUST00000115789] [ENSMUST00000115790] [ENSMUST00000115791] [ENSMUST00000134767] [ENSMUST00000142409] [ENSMUST00000146009]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000061091
AA Change: H275N

PolyPhen 2 Score 0.913 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000060382
Gene: ENSMUSG00000023805
AA Change: H275N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	263	2.5e-72	PFAM
Blast:IPPc	394	423	3e-6	BLAST
IPPc	443	785	3.72e-128	SMART
DUF1866	778	923	1.04e-73	SMART
low complexity region	926	940	N/A	INTRINSIC
low complexity region	965	976	N/A	INTRINSIC
low complexity region	1012	1027	N/A	INTRINSIC
low complexity region	1127	1139	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000080283
AA Change: H360N

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000079164
Gene: ENSMUSG00000023805
AA Change: H360N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	60	348	5.5e-78	PFAM
Blast:IPPc	479	508	3e-6	BLAST
IPPc	528	870	3.72e-128	SMART
DUF1866	863	1008	1.04e-73	SMART
low complexity region	1011	1025	N/A	INTRINSIC
low complexity region	1050	1061	N/A	INTRINSIC
low complexity region	1167	1179	N/A	INTRINSIC
low complexity region	1217	1234	N/A	INTRINSIC
low complexity region	1263	1277	N/A	INTRINSIC
low complexity region	1293	1306	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000115784

SMART Domains

Protein: ENSMUSP00000111450
Gene: ENSMUSG00000023805

Domain	Start	End	E-Value	Type
PDB:3LWT\|X	9	171	3e-12	PDB
Blast:IPPc	163	192	2e-6	BLAST
IPPc	212	554	3.72e-128	SMART
DUF1866	547	692	1.04e-73	SMART
low complexity region	695	709	N/A	INTRINSIC
low complexity region	734	745	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115785
AA Change: H44N

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000111451
Gene: ENSMUSG00000023805
AA Change: H44N

Domain	Start	End	E-Value	Type
PDB:3LWT\|X	9	171	4e-12	PDB
Blast:IPPc	163	192	2e-6	BLAST
IPPc	212	554	3.72e-128	SMART
DUF1866	547	692	1.04e-73	SMART
low complexity region	695	709	N/A	INTRINSIC
low complexity region	734	745	N/A	INTRINSIC
low complexity region	851	863	N/A	INTRINSIC
low complexity region	901	918	N/A	INTRINSIC
low complexity region	947	961	N/A	INTRINSIC
low complexity region	977	990	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115786
AA Change: H120N

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000111452
Gene: ENSMUSG00000023805
AA Change: H120N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	108	5.3e-29	PFAM
Blast:IPPc	239	268	1e-6	BLAST
IPPc	288	525	6e-18	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000115787

SMART Domains

Protein: ENSMUSP00000111453
Gene: ENSMUSG00000023805

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	108	5.7e-28	PFAM
Blast:IPPc	239	268	2e-6	BLAST
IPPc	288	630	3.72e-128	SMART
DUF1866	623	768	1.04e-73	SMART
low complexity region	771	785	N/A	INTRINSIC
low complexity region	810	821	N/A	INTRINSIC
low complexity region	927	939	N/A	INTRINSIC
low complexity region	977	994	N/A	INTRINSIC
low complexity region	1023	1037	N/A	INTRINSIC
low complexity region	1053	1066	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000115788

SMART Domains

Protein: ENSMUSP00000111454
Gene: ENSMUSG00000023805

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	108	4.8e-28	PFAM
Blast:IPPc	239	268	2e-6	BLAST
IPPc	288	630	3.72e-128	SMART
DUF1866	623	768	1.04e-73	SMART
low complexity region	771	785	N/A	INTRINSIC
low complexity region	810	821	N/A	INTRINSIC
low complexity region	927	939	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000115789

SMART Domains

Protein: ENSMUSP00000111455
Gene: ENSMUSG00000023805

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	187	2.3e-60	PFAM
Blast:IPPc	318	347	2e-6	BLAST
IPPc	367	709	3.72e-128	SMART
DUF1866	702	847	1.04e-73	SMART
low complexity region	850	864	N/A	INTRINSIC
low complexity region	889	900	N/A	INTRINSIC
low complexity region	1006	1018	N/A	INTRINSIC
low complexity region	1056	1073	N/A	INTRINSIC
low complexity region	1102	1116	N/A	INTRINSIC
low complexity region	1132	1145	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115790
AA Change: H275N

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000111456
Gene: ENSMUSG00000023805
AA Change: H275N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	263	3e-72	PFAM
Blast:IPPc	394	423	3e-6	BLAST
IPPc	443	785	3.72e-128	SMART
DUF1866	778	923	1.04e-73	SMART
low complexity region	926	940	N/A	INTRINSIC
low complexity region	965	976	N/A	INTRINSIC
low complexity region	1012	1027	N/A	INTRINSIC
low complexity region	1127	1139	N/A	INTRINSIC
low complexity region	1177	1194	N/A	INTRINSIC
low complexity region	1223	1237	N/A	INTRINSIC
low complexity region	1253	1266	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115791
AA Change: H360N

PolyPhen 2 Score 0.530 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000111457
Gene: ENSMUSG00000023805
AA Change: H360N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	61	343	8.5e-67	PFAM
Blast:IPPc	479	508	3e-6	BLAST
IPPc	528	870	3.72e-128	SMART
DUF1866	863	1008	1.04e-73	SMART
low complexity region	1011	1025	N/A	INTRINSIC
low complexity region	1050	1061	N/A	INTRINSIC
low complexity region	1097	1112	N/A	INTRINSIC
low complexity region	1212	1224	N/A	INTRINSIC
low complexity region	1262	1279	N/A	INTRINSIC
low complexity region	1308	1322	N/A	INTRINSIC
low complexity region	1338	1351	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130661

Predicted Effect

probably benign
Transcript: ENSMUST00000134767

Predicted Effect

probably benign
Transcript: ENSMUST00000142409
AA Change: H120N

PolyPhen 2 Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000120006
Gene: ENSMUSG00000023805
AA Change: H120N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	1	108	2.5e-28	PFAM
Blast:IPPc	239	268	2e-6	BLAST
IPPc	288	630	3.72e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000146009
AA Change: H360N

PolyPhen 2 Score 0.089 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000122381
Gene: ENSMUSG00000023805
AA Change: H360N

Domain	Start	End	E-Value	Type
Pfam:Syja_N	60	348	3.6e-78	PFAM
Blast:IPPc	479	508	3e-6	BLAST
IPPc	528	870	3.72e-128	SMART
DUF1866	863	1008	1.04e-73	SMART
low complexity region	1011	1025	N/A	INTRINSIC
low complexity region	1050	1061	N/A	INTRINSIC
low complexity region	1097	1112	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232567

Meta Mutation Damage Score

0.0794

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.8%

Validation Efficiency

94% (62/66)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygotes for an ENU-induced allele show progressive hearing loss and cochlear hair cell degeneration associated with fusion of stereocilia followed by total loss of hair bundles and cochlear ganglion degeneration. No vestibular dysfunction or other behavioral deficits are observed. [provided by MGI curators]

Allele List at MGI

All alleles(5) : Targeted, other(1) Gene trapped(4)

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810474O19Rik	G	A	6: 149,331,507		probably null	Het
4930433I11Rik	T	A	7: 40,993,526	S297R	possibly damaging	Het
5530400C23Rik	A	G	6: 133,294,326	E111G	possibly damaging	Het
8030423J24Rik	T	A	13: 70,883,910	S34T	unknown	Het
Ace3	T	A	11: 105,994,732	W20R	possibly damaging	Het
Adgrf1	A	G	17: 43,310,687	E605G	probably damaging	Het
Arhgap44	G	A	11: 65,162,549		probably benign	Het
Atm	A	C	9: 53,490,959	H1404Q	probably benign	Het
AW209491	A	G	13: 14,636,721	E53G	probably damaging	Het
Cdt1	C	T	8: 122,571,368	T366I	probably benign	Het
Cerk	A	T	15: 86,142,773	C179S	probably benign	Het
Cldn10	T	C	14: 118,861,843	V123A	possibly damaging	Het
Clip1	T	C	5: 123,613,541	K726E	possibly damaging	Het
Dcaf12	A	T	4: 41,294,043	Y365N	probably damaging	Het
Dennd6b	A	G	15: 89,188,821	L171P	probably damaging	Het
Dip2c	G	A	13: 9,533,254	V91I	probably benign	Het
Dlec1	A	G	9: 119,143,319	I1431V	probably benign	Het
Egln1	T	C	8: 124,948,492	D188G	probably damaging	Het
Enpp5	T	A	17: 44,081,368	N229K	possibly damaging	Het
Fmo1	T	G	1: 162,836,298	I221L	probably benign	Het
Fsip2	G	A	2: 82,987,945	W4674*	probably null	Het
Gm12185	G	A	11: 48,908,428	Q413*	probably null	Het
Gm5096	G	A	18: 87,757,121	C256Y	probably damaging	Het
Gm7298	A	T	6: 121,764,927	H436L	probably benign	Het
Gucy2c	G	A	6: 136,740,686	Q430*	probably null	Het
Hgd	A	G	16: 37,613,298	H134R	probably damaging	Het
Hoxd8	A	G	2: 74,705,999	E151G	probably damaging	Het
Il15ra	A	G	2: 11,720,016	D99G	probably damaging	Het
Ints4	T	A	7: 97,509,583		probably null	Het
Itgb1	T	A	8: 128,720,283	F426L	possibly damaging	Het
Itpr1	A	C	6: 108,518,755	I2534L	probably benign	Het
Kcnq4	T	A	4: 120,716,559	H235L	probably damaging	Het
Kcnt1	T	A	2: 25,892,383	I178N	probably damaging	Het
Kidins220	A	G	12: 24,997,311	D252G	probably damaging	Het
Krt23	A	G	11: 99,485,718	I204T	probably damaging	Het
Lipo4	A	G	19: 33,503,293	L225P	probably damaging	Het
Lrp3	T	C	7: 35,204,123	D245G	possibly damaging	Het
Mmp16	A	G	4: 18,051,857	D282G	probably damaging	Het
Myo1c	A	T	11: 75,650,742	H18L	probably benign	Het
Myo1f	C	A	17: 33,604,344	P981Q	probably benign	Het
Nle1	A	T	11: 82,908,157	F33I	probably benign	Het
Nlrp4e	T	G	7: 23,321,306	M406R	probably damaging	Het
Obscn	A	T	11: 59,051,785	V4857E	probably damaging	Het
Palb2	A	T	7: 122,128,420		probably null	Het
Phospho1	A	T	11: 95,830,624	E22V	probably damaging	Het
Pom121l2	C	T	13: 21,983,668	S703L	possibly damaging	Het
Prex2	T	C	1: 10,993,851	L20P	probably damaging	Het
Psmb7	T	C	2: 38,643,381	T45A	probably damaging	Het
R3hdm2	T	C	10: 127,484,507	I532T	probably damaging	Het
Rcn1	T	C	2: 105,392,017	D208G	probably damaging	Het
Recql5	A	G	11: 115,932,787		probably null	Het
Rfc4	A	T	16: 23,114,683	I242N	probably damaging	Het
Rims1	T	C	1: 22,432,984	Y650C	probably damaging	Het
Shc2	C	T	10: 79,627,019		probably null	Het
Slc14a2	A	T	18: 78,158,975		probably null	Het
Slc6a6	A	T	6: 91,740,014		probably null	Het
T	A	T	17: 8,441,786	T410S	probably benign	Het
Tarsl2	A	G	7: 65,682,779	I543V	probably benign	Het
Tbc1d8	T	A	1: 39,372,403	K1117N	probably damaging	Het
Tm7sf3	A	T	6: 146,606,289	L425*	probably null	Het
Trav14-3	A	G	14: 53,763,521	Y63C	probably damaging	Het
Tyro3	A	C	2: 119,803,270	D133A	probably damaging	Het
Vmn1r119	T	G	7: 21,011,815	H214P	possibly damaging	Het
Vmn2r120	G	A	17: 57,509,418	P646S	probably benign	Het
Zbtb7c	A	T	18: 76,145,833	Y454F	probably benign	Het
Zmym2	T	C	14: 56,950,309	L1144P	probably damaging	Het

Other mutations in Synj2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01067:Synj2	APN	17	6037926	missense	possibly damaging	0.48
IGL01399:Synj2	APN	17	6009771	missense	probably damaging	1.00
IGL01793:Synj2	APN	17	6027225	nonsense	probably null
IGL01793:Synj2	APN	17	6038046	missense	probably benign	0.01
IGL02096:Synj2	APN	17	5990353	missense	probably damaging	1.00
IGL02115:Synj2	APN	17	6017590	missense	probably damaging	1.00
IGL02222:Synj2	APN	17	6037480	missense	probably benign	0.04
IGL02478:Synj2	APN	17	6037924	missense	probably benign	0.00
IGL02634:Synj2	APN	17	6029760	missense	probably damaging	1.00
IGL02652:Synj2	APN	17	6017593	missense	probably damaging	1.00
IGL02681:Synj2	APN	17	5990336	missense	probably damaging	1.00
IGL02719:Synj2	APN	17	5996917	missense	probably benign	0.02
IGL03253:Synj2	APN	17	6003159	splice site	probably null
IGL03365:Synj2	APN	17	6019404	missense	probably damaging	1.00
I2288:Synj2	UTSW	17	6022267	splice site	probably benign
I2289:Synj2	UTSW	17	6022267	splice site	probably benign
R0389:Synj2	UTSW	17	6029783	missense	probably benign	0.35
R0433:Synj2	UTSW	17	6033848	missense	probably damaging	1.00
R0530:Synj2	UTSW	17	6008105	missense	possibly damaging	0.88
R0539:Synj2	UTSW	17	5996888	start codon destroyed	probably null	0.63
R0556:Synj2	UTSW	17	6037955	nonsense	probably null
R1263:Synj2	UTSW	17	6019359	missense	probably damaging	0.99
R1443:Synj2	UTSW	17	6023665	missense	probably damaging	0.99
R1450:Synj2	UTSW	17	6027324	splice site	probably benign
R1532:Synj2	UTSW	17	6033919	missense	probably benign	0.00
R1542:Synj2	UTSW	17	6025017	missense	probably benign	0.01
R1809:Synj2	UTSW	17	6026551	missense	possibly damaging	0.95
R1875:Synj2	UTSW	17	6028550	missense	possibly damaging	0.69
R1897:Synj2	UTSW	17	6022137	nonsense	probably null
R1928:Synj2	UTSW	17	5990267	missense	probably damaging	0.99
R2008:Synj2	UTSW	17	5996946	missense	probably damaging	1.00
R2060:Synj2	UTSW	17	6037480	missense	probably benign	0.04
R2109:Synj2	UTSW	17	6013691	missense	probably benign	0.00
R2332:Synj2	UTSW	17	6023794	missense	probably damaging	0.99
R2413:Synj2	UTSW	17	6028574	missense	probably damaging	1.00
R3684:Synj2	UTSW	17	6028443	missense	probably damaging	0.97
R4111:Synj2	UTSW	17	6007965	missense	probably benign	0.02
R4113:Synj2	UTSW	17	6007965	missense	probably benign	0.02
R4654:Synj2	UTSW	17	6013538	missense	probably damaging	1.00
R4797:Synj2	UTSW	17	6033888	missense	probably damaging	1.00
R4812:Synj2	UTSW	17	6010664	missense	probably damaging	1.00
R4873:Synj2	UTSW	17	5988068	intron	probably benign
R4875:Synj2	UTSW	17	5988068	intron	probably benign
R5110:Synj2	UTSW	17	6037715	missense	probably benign	0.06
R5205:Synj2	UTSW	17	5941518	missense	probably damaging	1.00
R5504:Synj2	UTSW	17	6036475	missense	possibly damaging	0.85
R5593:Synj2	UTSW	17	6038115	makesense	probably null
R5690:Synj2	UTSW	17	6035527	missense	probably benign	0.00
R5870:Synj2	UTSW	17	6037853	missense	probably benign	0.00
R6084:Synj2	UTSW	17	6017614	missense	probably damaging	0.98
R6084:Synj2	UTSW	17	6038098	missense	probably damaging	1.00
R6158:Synj2	UTSW	17	5986212	missense	probably benign	0.00
R6159:Synj2	UTSW	17	5986052	missense	probably damaging	1.00
R6278:Synj2	UTSW	17	5975874	missense	probably damaging	1.00
R6406:Synj2	UTSW	17	6019571	intron	probably benign
R6531:Synj2	UTSW	17	6033839	missense	probably damaging	1.00
R6729:Synj2	UTSW	17	5986014	start codon destroyed	probably null	1.00
R6774:Synj2	UTSW	17	6038015	missense	possibly damaging	0.87
R6792:Synj2	UTSW	17	5990290	missense	probably benign	0.01
R6844:Synj2	UTSW	17	5975806	missense	probably damaging	0.96
R6865:Synj2	UTSW	17	6017569	nonsense	probably null
R7178:Synj2	UTSW	17	6026479	missense	possibly damaging	0.95
R7286:Synj2	UTSW	17	6037945	missense	possibly damaging	0.79
R7403:Synj2	UTSW	17	6037730	missense	possibly damaging	0.76
R7451:Synj2	UTSW	17	6029791	missense	possibly damaging	0.68
R7501:Synj2	UTSW	17	5990239	missense	possibly damaging	0.79
R7730:Synj2	UTSW	17	6016287	missense	probably benign	0.33
R7799:Synj2	UTSW	17	6037823	missense	probably benign	0.10
R7804:Synj2	UTSW	17	6019534	missense	unknown
R7841:Synj2	UTSW	17	6044144	missense	unknown
R8347:Synj2	UTSW	17	6009785	missense	probably damaging	1.00
R8358:Synj2	UTSW	17	6023805	nonsense	probably null
R8391:Synj2	UTSW	17	5941521	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CCACAGCTAATGTACTCTAGTGGG -3'
(R):5'- TCAGGAAACCACAAGTGCAG -3'

Sequencing Primer
(F):5'- CAGAGGAAGAGCTTTCAACTCCTTTC -3'
(R):5'- AAGTGCAGCCAGGCAGTC -3'

Posted On

2017-10-10