Mutagenetix > Incidental Mutation

Incidental Mutation 'R3946:Synj1'

307730

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

MMRRC Submission

040827-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R3946 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

90936092-91011308 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 91010096 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 58 (F58L)

Ref Sequence

ENSEMBL: ENSMUSP00000113308 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000118522] [ENSMUST00000121759] [ENSMUST00000130813] [ENSMUST00000170853]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000023698

SMART Domains

Protein: ENSMUSP00000023698
Gene: ENSMUSG00000022974

Domain	Start	End	E-Value	Type
low complexity region	5	27	N/A	INTRINSIC
low complexity region	51	57	N/A	INTRINSIC
low complexity region	60	86	N/A	INTRINSIC
low complexity region	123	136	N/A	INTRINSIC
low complexity region	195	208	N/A	INTRINSIC
low complexity region	434	444	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000118246

Predicted Effect

unknown
Transcript: ENSMUST00000118390
AA Change: F32L

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: F32L

Domain	Start	End	E-Value	Type
low complexity region	1	15	N/A	INTRINSIC
Pfam:Syja_N	75	356	3.1e-71	PFAM
IPPc	546	889	6.37e-177	SMART
DUF1866	882	1024	1.24e-80	SMART
low complexity region	1040	1069	N/A	INTRINSIC
low complexity region	1117	1151	N/A	INTRINSIC
low complexity region	1155	1166	N/A	INTRINSIC
low complexity region	1189	1208	N/A	INTRINSIC
low complexity region	1289	1322	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000118522

SMART Domains

Protein: ENSMUSP00000113835
Gene: ENSMUSG00000022974

Domain	Start	End	E-Value	Type
coiled coil region	3	28	N/A	INTRINSIC
low complexity region	114	120	N/A	INTRINSIC
low complexity region	123	149	N/A	INTRINSIC
low complexity region	186	199	N/A	INTRINSIC
low complexity region	258	271	N/A	INTRINSIC
low complexity region	525	546	N/A	INTRINSIC
Pfam:GCFC	597	812	5.1e-39	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000121759
AA Change: F58L

PolyPhen 2 Score 0.482 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: F58L

Domain	Start	End	E-Value	Type
low complexity region	9	40	N/A	INTRINSIC
Pfam:Syja_N	100	381	4.2e-71	PFAM
IPPc	571	914	6.37e-177	SMART
DUF1866	907	1049	1.24e-80	SMART
low complexity region	1065	1094	N/A	INTRINSIC
low complexity region	1142	1176	N/A	INTRINSIC
low complexity region	1180	1191	N/A	INTRINSIC
low complexity region	1214	1233	N/A	INTRINSIC
low complexity region	1314	1343	N/A	INTRINSIC
Blast:IPPc	1344	1428	1e-17	BLAST
low complexity region	1564	1596	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125902

Predicted Effect

probably benign
Transcript: ENSMUST00000130813
AA Change: F18L

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973
AA Change: F18L

Domain	Start	End	E-Value	Type
Pfam:Syja_N	59	346	1.4e-86	PFAM
low complexity region	441	459	N/A	INTRINSIC
IPPc	526	693	1.8e-9	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154854

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156140

Predicted Effect

probably benign
Transcript: ENSMUST00000170853
AA Change: F18L

PolyPhen 2 Score 0.085 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: F18L

Domain	Start	End	E-Value	Type
Pfam:Syja_N	59	346	1.7e-85	PFAM
IPPc	531	874	6.37e-177	SMART
DUF1866	867	1009	1.24e-80	SMART
low complexity region	1025	1054	N/A	INTRINSIC
low complexity region	1102	1136	N/A	INTRINSIC
low complexity region	1140	1151	N/A	INTRINSIC
low complexity region	1174	1193	N/A	INTRINSIC
low complexity region	1274	1307	N/A	INTRINSIC

Meta Mutation Damage Score

0.0984

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.1%

Validation Efficiency

98% (60/61)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit neurological defects associated with impaired phosphoinositide metabolism and accumulation of clathrin-coated vesicles at nerve endings. Mutants show impaired suckling and most die within 24 hours of birth. [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
Aaed1	T	C	13: 64,309,098	I104V	probably damaging	Het
Abi2	A	G	1: 60,453,754	Q328R	probably damaging	Het
Agr3	C	A	12: 35,947,513		probably benign	Het
Brca2	T	A	5: 150,536,704	S481R	probably damaging	Het
Cabin1	T	G	10: 75,745,259	Q411P	probably damaging	Het
Calr3	A	G	8: 72,443,620	Y22H	probably damaging	Het
Caprin1	T	A	2: 103,796,766	I59F	probably damaging	Het
Cdk5rap1	T	C	2: 154,348,716	T442A	probably damaging	Het
Chn2	T	C	6: 54,269,426		probably benign	Het
Cic	C	A	7: 25,272,346	R501S	possibly damaging	Het
Coch	A	G	12: 51,601,812		probably null	Het
Defa25	G	A	8: 21,084,490	V17I	probably null	Het
Dglucy	T	C	12: 100,838,700		probably null	Het
Dtx1	T	G	5: 120,681,286	T616P	possibly damaging	Het
Eef1g	T	C	19: 8,969,977	L171P	probably benign	Het
Fam135a	A	G	1: 24,030,394	S465P	probably damaging	Het
Gm14025	A	G	2: 129,039,601	L135P	probably damaging	Het
Gm14412	A	T	2: 177,314,685	C472*	probably null	Het
Gm7104	T	C	12: 88,286,042		noncoding transcript	Het
Got2	A	G	8: 95,888,230	S26P	probably benign	Het
H2-M11	A	G	17: 36,549,231	I329M	probably damaging	Het
Hmcn2	T	A	2: 31,382,394	D1295E	possibly damaging	Het
Hoxd12	G	T	2: 74,675,427	R114L	probably damaging	Het
Ilkap	A	C	1: 91,387,250	D124E	probably damaging	Het
Med6	T	C	12: 81,581,851	Y88C	probably damaging	Het
Mep1a	A	T	17: 43,475,041	L719*	probably null	Het
Mmp23	T	C	4: 155,652,023	Y187C	probably damaging	Het
Myo1g	A	G	11: 6,520,760	M32T	possibly damaging	Het
Ncstn	T	C	1: 172,067,494	E614G	probably benign	Het
Nr2c2	C	T	6: 92,163,138	R464W	probably damaging	Het
Olfr1309	G	A	2: 111,983,297	T259M	possibly damaging	Het
Otub2	T	A	12: 103,392,826	L58*	probably null	Het
Pcdhga12	G	A	18: 37,767,629	V505I	probably benign	Het
Pcdhga9	T	A	18: 37,737,844	V242D	probably damaging	Het
Pex1	C	T	5: 3,626,084	L891F	probably damaging	Het
Pgm1	C	T	5: 64,112,061	T497I	probably benign	Het
Pikfyve	T	C	1: 65,196,681	F171L	probably damaging	Het
Pilrb1	T	G	5: 137,857,392	K79T	probably benign	Het
Pin1	C	T	9: 20,655,364	R21W	probably damaging	Het
Ptprq	A	G	10: 107,686,392		probably benign	Het
Rad17	G	A	13: 100,622,863	A552V	possibly damaging	Het
Rbbp8	A	G	18: 11,718,868	T249A	probably benign	Het
Rtkn	A	T	6: 83,135,976	I10F	probably benign	Het
Scube2	T	A	7: 109,857,590	I103F	possibly damaging	Het
Sec23b	A	G	2: 144,581,973	H514R	probably benign	Het
Serbp1	T	A	6: 67,272,220	D223E	probably benign	Het
Slc14a1	C	A	18: 78,111,392	V260L	probably benign	Het
Slc22a23	A	G	13: 34,183,126	I633T	probably damaging	Het
Stk19	A	T	17: 34,824,747		probably benign	Het
Svs2	T	C	2: 164,237,127	M287V	probably benign	Het
Syne3	T	A	12: 104,958,066	Q358L	probably damaging	Het
Tg	T	C	15: 66,674,023	V198A	probably damaging	Het
Tle4	A	T	19: 14,597,388	Y9N	probably damaging	Het
Tmem57	A	G	4: 134,804,481	Y626H	probably damaging	Het
Tmx3	G	A	18: 90,524,335	A186T	possibly damaging	Het
Traf3	G	A	12: 111,255,245	S280N	possibly damaging	Het
Trmt13	A	G	3: 116,581,518	F447S	probably damaging	Het
Trp53bp1	T	A	2: 121,228,626	H918L	probably damaging	Het
Ush2a	T	G	1: 188,728,504	V2654G	probably benign	Het
Vmn2r25	A	G	6: 123,840,098	Y175H	probably damaging	Het
Zfp335	T	C	2: 164,892,189	D1330G	probably damaging	Het

Other mutations in Synj1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01143:Synj1	APN	16	90951976	missense	probably damaging	1.00
IGL01468:Synj1	APN	16	91010172	splice site	probably benign
IGL02209:Synj1	APN	16	90987419	missense	probably damaging	0.97
IGL02452:Synj1	APN	16	90961365	splice site	probably benign
IGL02619:Synj1	APN	16	90974045	missense	probably damaging	1.00
IGL02650:Synj1	APN	16	90976696	missense	probably benign	0.03
IGL02708:Synj1	APN	16	90991462	missense	probably damaging	1.00
IGL02863:Synj1	APN	16	90961434	missense	possibly damaging	0.94
IGL03131:Synj1	APN	16	90988168	missense	probably damaging	0.99
IGL03295:Synj1	APN	16	90938430	missense	probably benign	0.14
IGL03356:Synj1	APN	16	90987392	missense	probably damaging	1.00
PIT1430001:Synj1	UTSW	16	90964508	missense	probably damaging	1.00
R0179:Synj1	UTSW	16	90964631	missense	possibly damaging	0.80
R0396:Synj1	UTSW	16	90938640	missense	probably benign
R0426:Synj1	UTSW	16	90967354	missense	probably damaging	1.00
R0486:Synj1	UTSW	16	90938263	utr 3 prime	probably benign
R0515:Synj1	UTSW	16	90994022	missense	possibly damaging	0.93
R0535:Synj1	UTSW	16	90948087	missense	possibly damaging	0.80
R0697:Synj1	UTSW	16	90960615	missense	probably benign	0.44
R0698:Synj1	UTSW	16	90960615	missense	probably benign	0.44
R0945:Synj1	UTSW	16	90960445	missense	possibly damaging	0.90
R1327:Synj1	UTSW	16	90946855	missense	probably benign	0.05
R1562:Synj1	UTSW	16	90987402	missense	probably benign	0.09
R1732:Synj1	UTSW	16	90964230	missense	probably damaging	0.99
R1752:Synj1	UTSW	16	90938473	missense	probably benign
R1785:Synj1	UTSW	16	90964517	missense	probably damaging	1.00
R1786:Synj1	UTSW	16	90964517	missense	probably damaging	1.00
R2011:Synj1	UTSW	16	90938696	missense	probably damaging	1.00
R2012:Synj1	UTSW	16	90938696	missense	probably damaging	1.00
R2065:Synj1	UTSW	16	90991649	critical splice acceptor site	probably null
R2862:Synj1	UTSW	16	90969329	missense	probably damaging	1.00
R3026:Synj1	UTSW	16	90978734	missense	probably damaging	1.00
R3151:Synj1	UTSW	16	90960626	missense	probably damaging	0.96
R3971:Synj1	UTSW	16	90991603	missense	probably damaging	1.00
R4472:Synj1	UTSW	16	90969181	critical splice donor site	probably null
R4547:Synj1	UTSW	16	90988282	missense	possibly damaging	0.51
R4647:Synj1	UTSW	16	90973989	missense	probably damaging	1.00
R4739:Synj1	UTSW	16	90955419	missense	probably benign	0.00
R5027:Synj1	UTSW	16	90940519	splice site	probably null
R5428:Synj1	UTSW	16	90991518	missense	probably damaging	0.98
R5586:Synj1	UTSW	16	91009977	intron	probably benign
R5769:Synj1	UTSW	16	90938253	utr 3 prime	probably benign
R6005:Synj1	UTSW	16	90969286	missense	probably damaging	1.00
R6119:Synj1	UTSW	16	90938989	missense	probably benign	0.30
R6313:Synj1	UTSW	16	90946815	missense	probably benign	0.00
R6324:Synj1	UTSW	16	90938630	missense	probably benign	0.00
R6549:Synj1	UTSW	16	90938677	missense	probably benign
R6696:Synj1	UTSW	16	90960452	missense	probably damaging	0.98
R6698:Synj1	UTSW	16	90960452	missense	probably damaging	0.98
R6861:Synj1	UTSW	16	90963880	nonsense	probably null
R7008:Synj1	UTSW	16	90993945	missense	probably damaging	1.00
R7153:Synj1	UTSW	16	90948090	missense	probably benign	0.04
R7393:Synj1	UTSW	16	90951999	missense	probably damaging	0.99
R7510:Synj1	UTSW	16	90938677	missense	probably benign
R7560:Synj1	UTSW	16	90940483	missense	probably benign
R7724:Synj1	UTSW	16	90961499	missense	probably damaging	0.99
R7913:Synj1	UTSW	16	90991427	missense	possibly damaging	0.83
R8326:Synj1	UTSW	16	90988196	missense	probably benign	0.12
R8707:Synj1	UTSW	16	90955431	missense	probably benign	0.02
R8711:Synj1	UTSW	16	91010083	missense	probably damaging	0.98
R8767:Synj1	UTSW	16	90961518	missense	probably damaging	1.00
R8911:Synj1	UTSW	16	90978734	missense	probably damaging	1.00
R9052:Synj1	UTSW	16	90938840	missense	probably benign	0.00
R9124:Synj1	UTSW	16	90938625	missense	probably benign	0.00
R9307:Synj1	UTSW	16	90988207	missense	probably damaging	0.98
R9408:Synj1	UTSW	16	90944852	missense	probably benign	0.27
R9458:Synj1	UTSW	16	90969312	missense	probably benign	0.05
R9567:Synj1	UTSW	16	90994024	missense	possibly damaging	0.79
R9651:Synj1	UTSW	16	90938524	missense	probably benign	0.00
R9651:Synj1	UTSW	16	90960455	missense	possibly damaging	0.56
R9707:Synj1	UTSW	16	90961412	missense	possibly damaging	0.91
R9730:Synj1	UTSW	16	90960664	missense	probably damaging	0.98
R9732:Synj1	UTSW	16	90964526	missense	probably damaging	1.00
Z1176:Synj1	UTSW	16	90987340	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTCAGAAGATCAAATTCAGGG -3'
(R):5'- TAAACCGTTCACCCCTGAGC -3'

Sequencing Primer
(F):5'- GATCAAATTCAGGGAGAAGGTTC -3'
(R):5'- GTTCACCCCTGAGCTCTCTTTTTC -3'

Posted On

2015-04-17