Mutagenetix > Incidental Mutation

Incidental Mutation 'R6698:Synj1'

528667

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

A930006D20Rik

MMRRC Submission

044816-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6698 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

90732980-90808196 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 90757340 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Leucine at position 877 (V877L)

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

probably damaging
Transcript: ENSMUST00000118390
AA Change: V877L

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: V877L

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: V903L

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: V903L

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: V863L

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: V863L

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

Meta Mutation Damage Score

0.1066

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.0%

Validation Efficiency

95% (40/42)

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Brca2	T	C	5: 150,455,859 (GRCm39)	V200A	probably damaging	Het
Camk2g	T	A	14: 20,792,776 (GRCm39)	K393*	probably null	Het
Catsperb	T	A	12: 101,475,466 (GRCm39)	F337I	probably damaging	Het
Cdk17	T	C	10: 93,064,540 (GRCm39)	Y270H	probably damaging	Het
Col5a3	C	T	9: 20,690,329 (GRCm39)	G1162R	probably damaging	Het
Col6a5	T	A	9: 105,811,374 (GRCm39)	N715I	unknown	Het
Fancg	A	G	4: 43,007,034 (GRCm39)	S248P	probably benign	Het
Flvcr1	T	C	1: 190,757,929 (GRCm39)	Y79C	probably damaging	Het
Gabrp	A	G	11: 33,507,017 (GRCm39)	S198P	probably damaging	Het
Gask1b	A	G	3: 79,843,902 (GRCm39)	I10V	probably damaging	Het
Glp1r	A	G	17: 31,155,375 (GRCm39)	Y454C	probably damaging	Het
Gpr158	A	C	2: 21,831,921 (GRCm39)	D1007A	probably damaging	Het
Gsdmc3	A	G	15: 63,732,120 (GRCm39)	F302S	possibly damaging	Het
Gsdmc4	T	A	15: 63,765,613 (GRCm39)	D312V	probably benign	Het
Itga5	T	C	15: 103,259,808 (GRCm39)	Y663C	probably benign	Het
Kif1b	A	T	4: 149,359,413 (GRCm39)	M108K	probably damaging	Het
Klf11	T	G	12: 24,703,618 (GRCm39)	S18A	probably damaging	Het
Lmtk2	T	C	5: 144,111,737 (GRCm39)	V819A	probably benign	Het
Lrba	A	G	3: 86,211,732 (GRCm39)	M451V	probably damaging	Het
Lrp1b	T	C	2: 41,192,958 (GRCm39)	D488G	probably damaging	Het
Mark4	T	C	7: 19,163,362 (GRCm39)	N589S	probably benign	Het
Mis12	T	C	11: 70,916,012 (GRCm39)	F15S	probably damaging	Het
Nif3l1	A	G	1: 58,489,648 (GRCm39)	D179G	probably benign	Het
Nlrx1	A	G	9: 44,177,104 (GRCm39)	W3R	probably damaging	Het
Nup210l	G	A	3: 90,089,815 (GRCm39)	S1194N	possibly damaging	Het
Or13m2-ps1	A	T	6: 42,778,136 (GRCm39)	T154S	probably benign	Het
Or5d20-ps1	A	G	2: 87,931,561 (GRCm39)	F257L	unknown	Het
Pnkd	T	A	1: 74,389,836 (GRCm39)	L320Q	probably damaging	Het
Prkn	A	G	17: 11,286,183 (GRCm39)		probably null	Het
Rcc2	G	A	4: 140,429,586 (GRCm39)	C40Y	probably benign	Homo
Rilpl2	C	T	5: 124,607,843 (GRCm39)	E126K	probably damaging	Het
Rpn2	T	C	2: 157,139,330 (GRCm39)	I208T	possibly damaging	Het
Skint4	G	T	4: 111,977,096 (GRCm39)	C170F	probably damaging	Het
Tcp11	A	T	17: 28,290,804 (GRCm39)	I106N	possibly damaging	Het
Tg	A	G	15: 66,711,211 (GRCm39)	Y991C	probably damaging	Het
Trib3	A	G	2: 152,180,339 (GRCm39)	S285P	probably damaging	Het
Wdr49	A	T	3: 75,336,673 (GRCm39)	W345R	probably benign	Het
Wnt5a	A	G	14: 28,240,420 (GRCm39)	Y190C	possibly damaging	Het
Xpo1	A	G	11: 23,244,040 (GRCm39)	E955G	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
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'- ACCAAAGTGTGCAAACTGCC -3'
(R):5'- CTCCTGAATGCTAGTTTCCAAGATG -3'

Sequencing Primer
(F):5'- TGCCGCAGAAGCTCATC -3'
(R):5'- AAAATTCTTTATACATGGACCCCTGG -3'

Posted On

2018-07-24