Mutagenetix > Incidental Mutation

Incidental Mutation 'R7153:Synj1'

554283

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7153 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

90936092-91011308 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 90948090 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Arginine at position 1189 (G1189R)

Ref Sequence

ENSEMBL: ENSMUSP00000113308 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000121759] [ENSMUST00000129743] [ENSMUST00000170853]

AlphaFold

no structure available at present

Predicted Effect

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: G1163R

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: ENSMUST00000121759
AA Change: G1189R

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: G1189R

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

probably benign
Transcript: ENSMUST00000125032

SMART Domains

Protein: ENSMUSP00000120399
Gene: ENSMUSG00000022973

Domain	Start	End	E-Value	Type
low complexity region	3	32	N/A	INTRINSIC
low complexity region	80	110	N/A	INTRINSIC
low complexity region	123	142	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000129743

SMART Domains

Protein: ENSMUSP00000123231
Gene: ENSMUSG00000022973

Domain	Start	End	E-Value	Type
low complexity region	69	101	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000154276

SMART Domains

Protein: ENSMUSP00000122675
Gene: ENSMUSG00000022973

Domain	Start	End	E-Value	Type
low complexity region	2	32	N/A	INTRINSIC
low complexity region	54	73	N/A	INTRINSIC
low complexity region	154	187	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000170853
AA Change: G1149R

PolyPhen 2 Score 0.940 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: G1149R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000231524

Meta Mutation Damage Score

0.0728

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

100% (75/75)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ano2	A	G	6: 125,992,943	T741A	possibly damaging	Het
Aox4	T	C	1: 58,250,219	M767T	probably damaging	Het
Arhgap39	C	A	15: 76,765,491	S27I	probably benign	Het
AU018091	T	A	7: 3,159,513	M296L	probably benign	Het
Axin1	A	G	17: 26,187,968	T512A	probably benign	Het
B4galnt3	A	T	6: 120,214,968	D602E	probably benign	Het
Bcl6	G	A	16: 23,966,226	R675*	probably null	Het
Bsnd	A	T	4: 106,492,033	D3E	probably benign	Het
Btbd18	C	T	2: 84,666,428	R137*	probably null	Het
C2cd5	A	G	6: 143,019,409	S871P	probably benign	Het
Cobl	G	T	11: 12,254,128	P858Q	probably damaging	Het
Col6a1	C	T	10: 76,710,341		probably null	Het
Crb2	A	T	2: 37,787,408	H304L	probably benign	Het
Crybg1	T	A	10: 43,964,666	Y1812F	possibly damaging	Het
Ddx60	A	T	8: 61,988,108	K1070N	possibly damaging	Het
Defb22	T	C	2: 152,485,920	K115R	unknown	Het
Dhx8	C	T	11: 101,740,175		probably null	Het
Dnah5	T	A	15: 28,365,522		probably null	Het
Dnah7b	T	A	1: 46,126,804	F543Y	probably benign	Het
Ehhadh	A	G	16: 21,766,321	F270S	probably damaging	Het
Esyt2	A	G	12: 116,346,508	M397V	probably benign	Het
Fanca	A	T	8: 123,316,425	L74H	probably damaging	Het
Fbxl17	C	A	17: 63,060,351	V676F	probably benign	Het
Fndc1	A	G	17: 7,801,645	V102A	probably damaging	Het
Gpalpp1	T	C	14: 76,095,011	Y273C	probably damaging	Het
Gpatch8	TTCCTCCTCCTCCTCTTCCTCCTCCTC	TTCCTCCTCCTCCTCCTCTTCCTCCTCCTC	11: 102,480,188		probably benign	Het
Grik2	T	C	10: 49,535,367	H225R	probably benign	Het
Helz2	A	T	2: 181,231,285	S2411T	probably benign	Het
Hnmt	C	T	2: 24,014,341	A103T	probably damaging	Het
Ighv15-2	G	T	12: 114,564,590	Y114*	probably null	Het
Irak2	A	G	6: 113,678,709	H357R	probably benign	Het
Kcp	T	C	6: 29,499,015	E320G	probably damaging	Het
Kpna4	A	G	3: 69,089,798	L352S	probably damaging	Het
Krt36	G	A	11: 100,105,146	Q151*	probably null	Het
Krt77	G	A	15: 101,865,496	T241M	probably benign	Het
Lca5l	T	A	16: 96,173,809	N305I	probably damaging	Het
Lefty1	T	A	1: 180,937,767	L300Q	probably benign	Het
Mertk	A	G	2: 128,736,649	Y185C	probably damaging	Het
Mmp14	T	C	14: 54,436,251	I124T	possibly damaging	Het
Nlrc4	T	C	17: 74,447,103	E95G	possibly damaging	Het
Npc1	A	G	18: 12,213,291	F283L	possibly damaging	Het
Olfr1180	A	C	2: 88,412,118	L180W	probably damaging	Het
Olfr1282	A	T	2: 111,335,901	M59K	probably damaging	Het
Pcdha11	T	C	18: 37,011,225	V123A	probably damaging	Het
Pcdhga2	T	C	18: 37,669,208	V35A	probably damaging	Het
Pgd	G	T	4: 149,161,678	T94K	probably benign	Het
Pik3c2a	T	C	7: 116,342,252	N1593S	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 109,624,195		probably benign	Het
Plcb3	A	G	19: 6,958,084		probably null	Het
Prkd3	C	T	17: 78,966,355	D491N	probably benign	Het
Ptprf	T	C	4: 118,231,543	T688A	probably damaging	Het
Pycr2	T	A	1: 180,906,682	L210M	probably damaging	Het
Rpl36	T	C	17: 56,614,137	I81T	probably benign	Het
Rraga	C	T	4: 86,576,016	A33V	probably damaging	Het
Slc29a1	G	A	17: 45,585,762	A429V	probably damaging	Het
Stab1	T	G	14: 31,160,584	E432A	probably benign	Het
Synpo2	A	G	3: 123,112,404	*1088Q	probably null	Het
Tbc1d21	T	C	9: 58,363,093	D133G	probably damaging	Het
Tenm2	A	G	11: 36,024,182	V2176A	probably damaging	Het
Tff1	A	G	17: 31,162,798	I35T	probably benign	Het
Thnsl1	T	C	2: 21,212,953	V506A	possibly damaging	Het
Timm10b	A	G	7: 105,640,880	Q50R	unknown	Het
Tjp2	A	T	19: 24,101,981	N843K	probably benign	Het
Tle1	A	T	4: 72,139,061	F101I	probably benign	Het
Tmem225	T	C	9: 40,148,368	F15L	probably benign	Het
Trav12-3	T	C	14: 53,622,161	L88P	probably benign	Het
Ttc7b	A	T	12: 100,355,034	W613R	probably damaging	Het
Ttn	T	A	2: 76,778,504	M17723L	probably benign	Het
Ttn	T	C	2: 76,945,316	D1840G	unknown	Het
Tubgcp2	T	C	7: 140,001,036	H668R	probably benign	Het
Ush2a	C	A	1: 188,728,484	N2647K	possibly damaging	Het
Vmn1r14	C	T	6: 57,233,866	S143F	probably benign	Het
Vmn2r70	A	G	7: 85,565,054	S297P	probably damaging	Het
Ywhab	T	C	2: 164,014,060	F119L	probably damaging	Het
Zmym2	T	A	14: 56,950,202	D1108E	probably benign	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
R3946:Synj1	UTSW	16	91010096	missense	possibly damaging	0.48
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
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'- AGCAAGCTCAGGGACACTAG -3'
(R):5'- GGTCAGTTTTGAGCTAAAGTCAC -3'

Sequencing Primer
(F):5'- GCTCAGGGACACTAGGGAAC -3'
(R):5'- CTGGAGCTCACTTTGTAGACCAG -3'

Posted On

2019-05-15