Mutagenetix > Incidental Mutation

Incidental Mutation 'R9707:Synj1'

729870

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

A930006D20Rik

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9707 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

90732980-90808196 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 90758300 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 848 (V848A)

Ref Sequence

ENSEMBL: ENSMUSP00000113308 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000121759] [ENSMUST00000130813] [ENSMUST00000170853] [ENSMUST00000231472]

AlphaFold

no structure available at present

Predicted Effect

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: V822A

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

possibly damaging
Transcript: ENSMUST00000121759
AA Change: V848A

PolyPhen 2 Score 0.907 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: V848A

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

SMART Domains

Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973

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

possibly damaging
Transcript: ENSMUST00000170853
AA Change: V808A

PolyPhen 2 Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: V808A

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: ENSMUST00000231472

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: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ambra1	G	A	2: 91,640,476 (GRCm39)	R635H	probably damaging	Het
Amz1	T	C	5: 140,733,949 (GRCm39)	V175A	possibly damaging	Het
Arsj	T	C	3: 126,232,160 (GRCm39)	I302T	possibly damaging	Het
Asxl3	A	G	18: 22,656,304 (GRCm39)	E1438G	probably benign	Het
BC016579	C	T	16: 45,460,760 (GRCm39)	E103K	probably damaging	Het
Ccdc54	T	A	16: 50,411,163 (GRCm39)	K34N	possibly damaging	Het
Chac2	T	C	11: 30,929,572 (GRCm39)	D55G	possibly damaging	Het
Cts3	T	A	13: 61,714,649 (GRCm39)	I219F	possibly damaging	Het
Des	A	G	1: 75,337,533 (GRCm39)	M158V	possibly damaging	Het
Dohh	T	C	10: 81,223,565 (GRCm39)	F206S	probably damaging	Het
Dst	T	C	1: 34,228,934 (GRCm39)	S2176P	probably benign	Het
Ecpas	C	T	4: 58,824,816 (GRCm39)		probably null	Het
Epb41l2	G	A	10: 25,378,235 (GRCm39)	V836M	probably damaging	Het
Foxc1	A	T	13: 31,991,882 (GRCm39)	E231V	probably damaging	Het
Ighd	T	A	12: 113,378,108 (GRCm39)	N164Y		Het
Ighv1-53	A	T	12: 115,122,035 (GRCm39)	Y113*	probably null	Het
Ildr1	A	G	16: 36,529,892 (GRCm39)	D93G	probably damaging	Het
Krt79	T	G	15: 101,839,196 (GRCm39)	E424D	probably benign	Het
Lrp1	T	C	10: 127,408,414 (GRCm39)	E1754G	probably benign	Het
Mbd4	T	A	6: 115,826,559 (GRCm39)	H144L	probably benign	Het
Mcm7	C	A	5: 138,170,000 (GRCm39)	A7S	probably benign	Het
Mmp9	T	A	2: 164,794,605 (GRCm39)	N532K	possibly damaging	Het
Msr1	T	G	8: 40,076,988 (GRCm39)	E207D	probably benign	Het
Neurl4	A	T	11: 69,799,679 (GRCm39)	D994V	probably damaging	Het
Or1e35	A	G	11: 73,798,090 (GRCm39)	V76A	possibly damaging	Het
Or6c69b	T	C	10: 129,627,444 (GRCm39)	T5A	probably damaging	Het
Or8s5	C	T	15: 98,238,154 (GRCm39)	V239I	probably benign	Het
Pcdhgb6	T	C	18: 37,876,768 (GRCm39)	I492T	possibly damaging	Het
Pde4c	A	G	8: 71,202,701 (GRCm39)	D669G	probably benign	Het
Phf3	C	A	1: 30,868,923 (GRCm39)		probably null	Het
Ptpn12	T	A	5: 21,207,620 (GRCm39)	T279S	probably damaging	Het
Rbbp6	A	T	7: 122,589,061 (GRCm39)	T287S	probably damaging	Het
Slc22a21	T	C	11: 53,851,186 (GRCm39)	N192S	probably benign	Het
Slc46a3	G	T	5: 147,821,022 (GRCm39)	H377N	probably benign	Het
Smg9	G	T	7: 24,102,869 (GRCm39)	R16L	probably damaging	Het
Spmip2	A	G	3: 79,313,167 (GRCm39)	I80M	probably damaging	Het
Taf7	A	T	18: 37,776,053 (GRCm39)	S171R	probably damaging	Het
Trav7-3	A	G	14: 53,681,189 (GRCm39)	E77G	probably benign	Het
Usp16	T	C	16: 87,263,235 (GRCm39)	S146P	probably benign	Het
Vmn1r22	A	T	6: 57,877,890 (GRCm39)	I29K	probably benign	Het
Zfp236	A	G	18: 82,664,328 (GRCm39)	C486R	probably damaging	Het
Zfp329	T	C	7: 12,544,129 (GRCm39)	Q465R	probably benign	Het

Other mutations in Synj1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01143:Synj1	APN	16	90,748,864 (GRCm39)	missense	probably damaging	1.00
IGL01468:Synj1	APN	16	90,807,060 (GRCm39)	splice site	probably benign
IGL02209:Synj1	APN	16	90,784,307 (GRCm39)	missense	probably damaging	0.97
IGL02452:Synj1	APN	16	90,758,253 (GRCm39)	splice site	probably benign
IGL02619:Synj1	APN	16	90,770,933 (GRCm39)	missense	probably damaging	1.00
IGL02650:Synj1	APN	16	90,773,584 (GRCm39)	missense	probably benign	0.03
IGL02708:Synj1	APN	16	90,788,350 (GRCm39)	missense	probably damaging	1.00
IGL02863:Synj1	APN	16	90,758,322 (GRCm39)	missense	possibly damaging	0.94
IGL03131:Synj1	APN	16	90,785,056 (GRCm39)	missense	probably damaging	0.99
IGL03295:Synj1	APN	16	90,735,318 (GRCm39)	missense	probably benign	0.14
IGL03356:Synj1	APN	16	90,784,280 (GRCm39)	missense	probably damaging	1.00
PIT1430001:Synj1	UTSW	16	90,761,396 (GRCm39)	missense	probably damaging	1.00
R0179:Synj1	UTSW	16	90,761,519 (GRCm39)	missense	possibly damaging	0.80
R0396:Synj1	UTSW	16	90,735,528 (GRCm39)	missense	probably benign
R0426:Synj1	UTSW	16	90,764,242 (GRCm39)	missense	probably damaging	1.00
R0486:Synj1	UTSW	16	90,735,151 (GRCm39)	utr 3 prime	probably benign
R0515:Synj1	UTSW	16	90,790,910 (GRCm39)	missense	possibly damaging	0.93
R0535:Synj1	UTSW	16	90,744,975 (GRCm39)	missense	possibly damaging	0.80
R0697:Synj1	UTSW	16	90,757,503 (GRCm39)	missense	probably benign	0.44
R0698:Synj1	UTSW	16	90,757,503 (GRCm39)	missense	probably benign	0.44
R0945:Synj1	UTSW	16	90,757,333 (GRCm39)	missense	possibly damaging	0.90
R1327:Synj1	UTSW	16	90,743,743 (GRCm39)	missense	probably benign	0.05
R1562:Synj1	UTSW	16	90,784,290 (GRCm39)	missense	probably benign	0.09
R1732:Synj1	UTSW	16	90,761,118 (GRCm39)	missense	probably damaging	0.99
R1752:Synj1	UTSW	16	90,735,361 (GRCm39)	missense	probably benign
R1785:Synj1	UTSW	16	90,761,405 (GRCm39)	missense	probably damaging	1.00
R1786:Synj1	UTSW	16	90,761,405 (GRCm39)	missense	probably damaging	1.00
R2011:Synj1	UTSW	16	90,735,584 (GRCm39)	missense	probably damaging	1.00
R2012:Synj1	UTSW	16	90,735,584 (GRCm39)	missense	probably damaging	1.00
R2065:Synj1	UTSW	16	90,788,537 (GRCm39)	critical splice acceptor site	probably null
R2862:Synj1	UTSW	16	90,766,217 (GRCm39)	missense	probably damaging	1.00
R3026:Synj1	UTSW	16	90,775,622 (GRCm39)	missense	probably damaging	1.00
R3151:Synj1	UTSW	16	90,757,514 (GRCm39)	missense	probably damaging	0.96
R3946:Synj1	UTSW	16	90,806,984 (GRCm39)	missense	possibly damaging	0.48
R3971:Synj1	UTSW	16	90,788,491 (GRCm39)	missense	probably damaging	1.00
R4472:Synj1	UTSW	16	90,766,069 (GRCm39)	critical splice donor site	probably null
R4547:Synj1	UTSW	16	90,785,170 (GRCm39)	missense	possibly damaging	0.51
R4647:Synj1	UTSW	16	90,770,877 (GRCm39)	missense	probably damaging	1.00
R4739:Synj1	UTSW	16	90,752,307 (GRCm39)	missense	probably benign	0.00
R5027:Synj1	UTSW	16	90,737,407 (GRCm39)	splice site	probably null
R5428:Synj1	UTSW	16	90,788,406 (GRCm39)	missense	probably damaging	0.98
R5586:Synj1	UTSW	16	90,806,865 (GRCm39)	intron	probably benign
R5769:Synj1	UTSW	16	90,735,141 (GRCm39)	utr 3 prime	probably benign
R6005:Synj1	UTSW	16	90,766,174 (GRCm39)	missense	probably damaging	1.00
R6119:Synj1	UTSW	16	90,735,877 (GRCm39)	missense	probably benign	0.30
R6313:Synj1	UTSW	16	90,743,703 (GRCm39)	missense	probably benign	0.00
R6324:Synj1	UTSW	16	90,735,518 (GRCm39)	missense	probably benign	0.00
R6549:Synj1	UTSW	16	90,735,565 (GRCm39)	missense	probably benign
R6696:Synj1	UTSW	16	90,757,340 (GRCm39)	missense	probably damaging	0.98
R6698:Synj1	UTSW	16	90,757,340 (GRCm39)	missense	probably damaging	0.98
R6861:Synj1	UTSW	16	90,760,768 (GRCm39)	nonsense	probably null
R7008:Synj1	UTSW	16	90,790,833 (GRCm39)	missense	probably damaging	1.00
R7153:Synj1	UTSW	16	90,744,978 (GRCm39)	missense	probably benign	0.04
R7393:Synj1	UTSW	16	90,748,887 (GRCm39)	missense	probably damaging	0.99
R7510:Synj1	UTSW	16	90,735,565 (GRCm39)	missense	probably benign
R7560:Synj1	UTSW	16	90,737,371 (GRCm39)	missense	probably benign
R7724:Synj1	UTSW	16	90,758,387 (GRCm39)	missense	probably damaging	0.99
R7913:Synj1	UTSW	16	90,788,315 (GRCm39)	missense	possibly damaging	0.83
R8326:Synj1	UTSW	16	90,785,084 (GRCm39)	missense	probably benign	0.12
R8707:Synj1	UTSW	16	90,752,319 (GRCm39)	missense	probably benign	0.02
R8711:Synj1	UTSW	16	90,806,971 (GRCm39)	missense	probably damaging	0.98
R8767:Synj1	UTSW	16	90,758,406 (GRCm39)	missense	probably damaging	1.00
R8911:Synj1	UTSW	16	90,775,622 (GRCm39)	missense	probably damaging	1.00
R9052:Synj1	UTSW	16	90,735,728 (GRCm39)	missense	probably benign	0.00
R9124:Synj1	UTSW	16	90,735,513 (GRCm39)	missense	probably benign	0.00
R9307:Synj1	UTSW	16	90,785,095 (GRCm39)	missense	probably damaging	0.98
R9408:Synj1	UTSW	16	90,741,740 (GRCm39)	missense	probably benign	0.27
R9458:Synj1	UTSW	16	90,766,200 (GRCm39)	missense	probably benign	0.05
R9567:Synj1	UTSW	16	90,790,912 (GRCm39)	missense	possibly damaging	0.79
R9651:Synj1	UTSW	16	90,757,343 (GRCm39)	missense	possibly damaging	0.56
R9651:Synj1	UTSW	16	90,735,412 (GRCm39)	missense	probably benign	0.00
R9730:Synj1	UTSW	16	90,757,552 (GRCm39)	missense	probably damaging	0.98
R9732:Synj1	UTSW	16	90,761,414 (GRCm39)	missense	probably damaging	1.00
Z1176:Synj1	UTSW	16	90,784,228 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCAGAACTGCAATCAGAAATTTTAC -3'
(R):5'- ACCTATAGGCCATGACCCAC -3'

Sequencing Primer
(F):5'- TCACTGAAAAATATGGGCATAAAATG -3'
(R):5'- CCACTGGGAGTCACATTAGGATTC -3'

Posted On

2022-10-06