Mutagenetix > Incidental Mutation

Incidental Mutation 'R0697:Synj1'

63906

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

A930006D20Rik

MMRRC Submission

038881-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0697 (G1)

Quality Score

118

Status

Not validated

Chromosome

Chromosomal Location

90732980-90808196 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 90757503 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 882 (T882A)

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

noncoding transcript
Transcript: ENSMUST00000118246

Predicted Effect

unknown
Transcript: ENSMUST00000118390
AA Change: T856A

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: T856A

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: T882A

PolyPhen 2 Score 0.440 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: T882A

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

probably benign
Transcript: ENSMUST00000170853
AA Change: T842A

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: T842A

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: 99.3%
3x: 98.8%
10x: 97.5%
20x: 95.4%

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: 21 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A1cf	C	A	19: 31,888,567 (GRCm39)	A99E	probably damaging	Het
Aig1	T	C	10: 13,705,069 (GRCm39)	N72S	probably benign	Het
Atad2	T	C	15: 57,968,939 (GRCm39)	I857M	possibly damaging	Het
Ceacam15	A	C	7: 16,407,445 (GRCm39)	L24*	probably null	Het
Cpsf2	A	G	12: 101,949,443 (GRCm39)	H53R	probably benign	Het
Crh	C	A	3: 19,748,241 (GRCm39)	G134C	probably damaging	Het
Cyp2g1	A	T	7: 26,514,152 (GRCm39)	K253*	probably null	Het
Dna2	T	C	10: 62,785,120 (GRCm39)	V79A	probably benign	Het
Dsc2	A	G	18: 20,174,509 (GRCm39)	V549A	probably damaging	Het
Etl4	G	T	2: 20,748,672 (GRCm39)	V135F	probably damaging	Het
Frk	A	G	10: 34,483,833 (GRCm39)	H398R	probably benign	Het
Gfra1	A	C	19: 58,258,555 (GRCm39)	S271A	probably benign	Het
Htr1b	T	C	9: 81,513,516 (GRCm39)	I364V	possibly damaging	Het
Kcnh5	A	T	12: 75,023,305 (GRCm39)	C588S	possibly damaging	Het
Kif13a	G	A	13: 47,001,813 (GRCm39)	T70I	probably benign	Het
Klra6	T	C	6: 129,993,687 (GRCm39)	I195V	probably benign	Het
Nras	T	C	3: 102,967,616 (GRCm39)	Y71H	possibly damaging	Het
Sirt5	T	C	13: 43,539,052 (GRCm39)	F274L	probably damaging	Het
Vmn1r84	A	T	7: 12,096,690 (GRCm39)	M1K	probably null	Het
Zfhx4	A	T	3: 5,466,793 (GRCm39)	E2317V	probably damaging	Het
Zfp345	A	T	2: 150,314,829 (GRCm39)	I236K	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
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
R9707:Synj1	UTSW	16	90,758,300 (GRCm39)	missense	possibly damaging	0.91
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'- TGATTGAGACCAGCACTGTGCC -3'
(R):5'- CTCAGACTGCTGAAGGTTCCAGAAG -3'

Sequencing Primer
(F):5'- ACCAGCACTGTGCCATCTG -3'
(R):5'- CTGAAGGTTCCAGAAGGAAGTAG -3'

Posted On

2013-07-30