Mutagenetix > Incidental Mutations

Incidental Mutation 'R7008:Synj1'

544860

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R7008 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

90936092-91011308 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 90993945 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 109 (N109K)

Ref Sequence

ENSEMBL: ENSMUSP00000113308 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: N83K

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 damaging
Transcript: ENSMUST00000121759
AA Change: N109K

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: N109K

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: ENSMUST00000130813
AA Change: N69K

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973
AA Change: N69K

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

probably benign
Transcript: ENSMUST00000170853
AA Change: N69K

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: N69K

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
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 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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd17	T	A	5: 90,260,096	I1421F	possibly damaging	Het
Arhgef11	C	A	3: 87,729,218	T992K	possibly damaging	Het
Arid1b	T	C	17: 5,290,979	Y853H	probably damaging	Het
Bcl10	G	T	3: 145,933,299	R232L	probably benign	Het
Best2	T	A	8: 85,013,211	I76F	possibly damaging	Het
Card11	G	C	5: 140,873,393	R1133G	probably damaging	Het
Card9	T	C	2: 26,357,799	D180G	possibly damaging	Het
Ccdc162	T	A	10: 41,552,415	E119V	probably damaging	Het
Cd2bp2	T	C	7: 127,195,395	D15G	possibly damaging	Het
Cdk7	A	C	13: 100,717,621	M120R	probably damaging	Het
Cryba4	T	A	5: 112,251,782	T2S	probably benign	Het
Cyp19a1	A	T	9: 54,193,325	M26K	probably benign	Het
Dgcr2	A	G	16: 17,845,001	S157P	probably damaging	Het
Dis3l	A	G	9: 64,310,453	F782S	possibly damaging	Het
Ephb4	T	A	5: 137,361,274	S369T	probably benign	Het
Fhad1	CGG	CG	4: 141,918,291		probably null	Het
Gm8251	T	C	1: 44,059,625	D771G	probably benign	Het
Hist1h1e	T	C	13: 23,622,209	K97E	probably damaging	Het
Igf2bp2	A	T	16: 22,081,832	D118E	probably benign	Het
Iqgap3	GGAGAG	GGAG	3: 88,112,771		probably null	Het
Klhl5	T	C	5: 65,143,249	S52P	probably benign	Het
Lrrc28	A	T	7: 67,595,711		probably benign	Het
Map4k4	T	G	1: 39,988,971	D317E	probably benign	Het
Maz	A	T	7: 127,024,612	C66S	probably damaging	Het
Mbd4	T	C	6: 115,850,724	T43A	possibly damaging	Het
Milr1	T	A	11: 106,751,314	S11T	probably damaging	Het
Mthfd2l	T	A	5: 90,959,728	C150S	probably damaging	Het
Nemf	A	T	12: 69,341,621	N325K	possibly damaging	Het
Nemf	C	T	12: 69,353,793		probably null	Het
Nod2	T	A	8: 88,663,657	C197*	probably null	Het
Odf2l	A	G	3: 145,132,734	K241E	probably damaging	Het
Olfr1427	G	A	19: 12,098,850	T263I	possibly damaging	Het
Olfr1489	A	T	19: 13,633,621	N170I	probably damaging	Het
Osbpl10	T	G	9: 115,061,848	D101E	probably damaging	Het
Osgin1	T	C	8: 119,441,494	V20A	possibly damaging	Het
Pan3	T	A	5: 147,545,693	C438S	probably damaging	Het
Plaa	A	G	4: 94,569,349	*795Q	probably null	Het
Prss35	T	C	9: 86,756,308	V377A	probably benign	Het
Rab5c	G	A	11: 100,719,963	R40C	probably damaging	Het
Rasl12	G	A	9: 65,410,869	V172M	probably damaging	Het
Rdh16f1	A	G	10: 127,790,906	H276R	probably benign	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Sez6l	T	C	5: 112,464,695	Y460C	probably damaging	Het
Sipa1l1	T	G	12: 82,363,112	M600R	probably damaging	Het
Slc11a2	T	C	15: 100,409,324	Y92C	probably damaging	Het
Slc4a10	A	G	2: 62,286,922	T712A	probably benign	Het
Sntb1	A	T	15: 55,792,072	Y249*	probably null	Het
Spatc1	A	G	15: 76,283,723	I127M	probably benign	Het
Tdg	T	A	10: 82,648,641	M396K	possibly damaging	Het
Tmem173	C	A	18: 35,735,171	R292L	probably damaging	Het
Tmem252	T	C	19: 24,674,292	V75A	probably damaging	Het
Trim40	T	C	17: 36,883,976	Q142R	probably damaging	Het
Trip6	T	C	5: 137,312,966	T163A	probably damaging	Het
Ttn	T	C	2: 76,894,642		probably benign	Het
Wdr95	T	C	5: 149,611,540	L721P	probably benign	Het
Zfp385c	A	T	11: 100,630,687	D182E	probably damaging	Het
Zfp597	A	G	16: 3,865,767	F375S	probably benign	Het
Zfp658	T	G	7: 43,573,912	F537C	possibly damaging	Het
Zgrf1	T	C	3: 127,561,772	F216L	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
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
Z1176:Synj1	UTSW	16	90987340	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTGCTTGACCAATGCATAGATAGG -3'
(R):5'- GGAAAACGATCCCATTTTGAAGC -3'

Sequencing Primer
(F):5'- TGACCAATGCATAGATAGGTTTGAG -3'
(R):5'- AGCTTTGTTTCAAGTCTGGCATTAC -3'

Posted On

2019-05-13