Mutagenetix > Incidental Mutation

Incidental Mutation 'R4739:Synj1'

359562

Institutional Source

Beutler Lab

Gene Symbol

Synj1

Ensembl Gene

ENSMUSG00000022973

Gene Name

synaptojanin 1

Synonyms

A930006D20Rik

MMRRC Submission

042025-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4739 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

90732980-90808196 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 90752307 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 1016 (H1016L)

Ref Sequence

ENSEMBL: ENSMUSP00000113308 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

unknown
Transcript: ENSMUST00000118390
AA Change: H990L

SMART Domains

Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: H990L

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: H1016L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: H1016L

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: 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

probably benign
Transcript: ENSMUST00000170853
AA Change: H976L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: H976L

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

noncoding transcript
Transcript: ENSMUST00000175515

Predicted Effect

probably benign
Transcript: ENSMUST00000231472

Predicted Effect

probably benign
Transcript: ENSMUST00000231524

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.5%

Validation Efficiency

96% (102/106)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1600012P17Rik	C	T	1: 158,796,904 (GRCm39)		noncoding transcript	Het
2300002M23Rik	A	G	17: 35,878,403 (GRCm39)		probably benign	Het
Aadat	T	C	8: 60,993,140 (GRCm39)	V360A	probably benign	Het
Abcc5	T	A	16: 20,218,376 (GRCm39)	D283V	probably damaging	Het
Abraxas1	T	A	5: 100,959,886 (GRCm39)	K155N	probably damaging	Het
Acot3	T	C	12: 84,105,364 (GRCm39)	I277T	probably benign	Het
Ankrd45	G	A	1: 160,982,960 (GRCm39)	C157Y	probably damaging	Het
Apol10a	C	T	15: 77,372,841 (GRCm39)	T159I	possibly damaging	Het
Arhgef11	G	A	3: 87,605,306 (GRCm39)	V214M	possibly damaging	Het
Ash1l	A	C	3: 88,890,152 (GRCm39)	N677T	probably benign	Het
Atg13	A	G	2: 91,515,040 (GRCm39)	S254P	probably damaging	Het
Atg16l2	A	G	7: 100,946,385 (GRCm39)	L129P	probably damaging	Het
Avl9	T	A	6: 56,703,294 (GRCm39)	V120D	probably damaging	Het
Castor1	A	G	11: 4,169,004 (GRCm39)	E57G	possibly damaging	Het
Cc2d1b	T	C	4: 108,485,239 (GRCm39)	V527A	probably benign	Het
Ccnl1	A	G	3: 65,854,092 (GRCm39)		probably benign	Het
Cenpl	T	A	1: 160,910,837 (GRCm39)	D261E	probably damaging	Het
Cep192	T	G	18: 67,984,803 (GRCm39)	I1604M	probably benign	Het
Cep95	A	G	11: 106,706,560 (GRCm39)	I573V	probably benign	Het
Cfap100	A	G	6: 90,389,825 (GRCm39)		probably null	Het
Ciao3	A	T	17: 26,000,283 (GRCm39)	H322L	probably damaging	Het
Cmc1	T	A	9: 117,904,245 (GRCm39)	M49L	probably benign	Het
Cyfip2	G	T	11: 46,170,820 (GRCm39)	N176K	probably damaging	Het
Cyp2w1	T	C	5: 139,342,430 (GRCm39)	F408L	probably damaging	Het
D630045J12Rik	G	A	6: 38,172,971 (GRCm39)	S399F	possibly damaging	Het
Dcbld2	T	A	16: 58,281,339 (GRCm39)	L528Q	probably damaging	Het
Dip2b	T	C	15: 100,105,658 (GRCm39)	V1138A	probably damaging	Het
Dip2c	T	A	13: 9,583,375 (GRCm39)	L119Q	probably damaging	Het
Dnah3	T	C	7: 119,677,169 (GRCm39)	D444G	possibly damaging	Het
Dsg1c	A	T	18: 20,408,246 (GRCm39)	N432Y	possibly damaging	Het
Dst	T	A	1: 34,230,228 (GRCm39)	I2785N	probably benign	Het
Dynap	A	T	18: 70,374,296 (GRCm39)	Y77N	possibly damaging	Het
Eif4g3	T	C	4: 137,910,510 (GRCm39)	L1330P	possibly damaging	Het
Eif4g3	T	A	4: 137,925,408 (GRCm39)	S1584T	probably benign	Het
Enpp1	A	T	10: 24,555,146 (GRCm39)	C67S	probably null	Het
Enpp5	C	T	17: 44,392,027 (GRCm39)	T152I	probably damaging	Het
Erbb4	T	C	1: 68,383,059 (GRCm39)	M313V	probably damaging	Het
Erc2	T	G	14: 27,498,838 (GRCm39)	L238R	probably damaging	Het
Eya3	T	A	4: 132,448,698 (GRCm39)		probably benign	Het
Farp1	T	C	14: 121,476,199 (GRCm39)	F339L	probably damaging	Het
Fsip2	A	C	2: 82,805,697 (GRCm39)	D672A	possibly damaging	Het
Gap43	G	T	16: 42,112,581 (GRCm39)	P60Q	probably benign	Het
Gpr37l1	T	A	1: 135,094,783 (GRCm39)	I154F	probably damaging	Het
Greb1	A	G	12: 16,746,329 (GRCm39)	S1314P	probably damaging	Het
Hectd4	A	T	5: 121,486,505 (GRCm39)	M3167L	probably benign	Het
Hps3	C	T	3: 20,084,574 (GRCm39)		probably null	Het
Hps5	A	G	7: 46,436,013 (GRCm39)	C178R	probably benign	Het
Hspg2	T	A	4: 137,297,384 (GRCm39)		probably benign	Het
Impdh2-ps	A	G	8: 100,757,839 (GRCm39)		noncoding transcript	Het
Josd2	T	A	7: 44,120,678 (GRCm39)	N138K	probably damaging	Het
Mtmr6	T	G	14: 60,529,546 (GRCm39)	M315R	probably damaging	Het
Mtrf1	G	A	14: 79,650,520 (GRCm39)	V323M	probably damaging	Het
Myo16	G	T	8: 10,423,527 (GRCm39)	G288W	probably damaging	Het
Myo18a	T	C	11: 77,714,149 (GRCm39)	Y748H	probably damaging	Het
Nek1	A	T	8: 61,551,545 (GRCm39)	N853I	probably benign	Het
Npnt	T	G	3: 132,610,452 (GRCm39)	T272P	possibly damaging	Het
Obi1	C	T	14: 104,747,819 (GRCm39)	D43N	probably damaging	Het
Or2ag1b	C	A	7: 106,288,351 (GRCm39)	E196*	probably null	Het
Or2b6	T	A	13: 21,823,340 (GRCm39)	M118L	possibly damaging	Het
Or2y17	G	A	11: 49,232,148 (GRCm39)	G263D	probably benign	Het
Or51e1	T	A	7: 102,359,378 (GRCm39)	I304N	probably damaging	Het
Or52n2c	G	A	7: 104,574,017 (GRCm39)	T318I	possibly damaging	Het
Or5a1	A	G	19: 12,097,234 (GRCm39)	Y269H	possibly damaging	Het
Pappa2	T	C	1: 158,784,582 (GRCm39)	R143G	probably benign	Het
Pappa2	T	G	1: 158,784,572 (GRCm39)	D146A	probably damaging	Het
Pcsk9	C	T	4: 106,304,353 (GRCm39)	G496R	probably damaging	Het
Pes1	A	G	11: 3,914,058 (GRCm39)	K8E	probably damaging	Het
Phlpp2	G	A	8: 110,667,052 (GRCm39)	G1194S	probably damaging	Het
Pkn1	A	C	8: 84,398,378 (GRCm39)	V763G	probably damaging	Het
Pkp2	C	A	16: 16,048,588 (GRCm39)	A331E	probably damaging	Het
Plb1	T	A	5: 32,507,023 (GRCm39)		probably null	Het
Plxna1	A	T	6: 89,309,657 (GRCm39)		probably null	Het
Polq	C	T	16: 36,862,109 (GRCm39)	T264M	probably damaging	Het
Prkag3	T	C	1: 74,779,864 (GRCm39)	*490W	probably null	Het
Prl2c1	T	C	13: 28,041,661 (GRCm39)	C228R	probably damaging	Het
Pus7l	T	C	15: 94,438,591 (GRCm39)	S85G	probably benign	Het
Rfc3	A	C	5: 151,568,241 (GRCm39)		probably benign	Het
Riox2	A	G	16: 59,309,732 (GRCm39)	N362S	probably benign	Het
Scaper	A	T	9: 55,650,932 (GRCm39)	D904E	probably damaging	Het
Scn11a	T	C	9: 119,583,627 (GRCm39)	M1663V	probably benign	Het
Slc13a3	A	T	2: 165,272,209 (GRCm39)	I278N	possibly damaging	Het
Slc22a7	T	C	17: 46,745,923 (GRCm39)	E278G	probably damaging	Het
Snrnp48	T	A	13: 38,393,893 (GRCm39)	M66K	probably damaging	Het
Styk1	T	G	6: 131,277,429 (GRCm39)	E404A	probably damaging	Het
Tbc1d8	G	A	1: 39,441,959 (GRCm39)	T211I	possibly damaging	Het
Tjp2	T	C	19: 24,097,475 (GRCm39)		probably null	Het
Tmem87a	A	G	2: 120,190,518 (GRCm39)		probably null	Het
Trappc9	T	G	15: 72,808,909 (GRCm39)	Y718S	probably damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ubqlnl	C	T	7: 103,798,925 (GRCm39)	V191M	probably benign	Het
Ugt2a3	C	T	5: 87,475,054 (GRCm39)	G397R	probably damaging	Het
Wdr33	T	A	18: 32,019,139 (GRCm39)	M454K	probably benign	Het
Wdtc1	G	T	4: 133,029,110 (GRCm39)	N325K	possibly damaging	Het
Whrn	T	C	4: 63,336,402 (GRCm39)	H720R	probably damaging	Het
Xirp2	A	T	2: 67,349,609 (GRCm39)	D3268V	probably damaging	Het
Zc3h7a	A	T	16: 10,959,573 (GRCm39)	H793Q	probably damaging	Het
Zfp518b	C	T	5: 38,831,841 (GRCm39)	A55T	possibly damaging	Het
Zmynd8	G	A	2: 165,647,249 (GRCm39)	T901M	probably damaging	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
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'- GAAACCCTTAGTGCTGGGACAAC -3'
(R):5'- TGGCCAGAGTGAAGGAATCC -3'

Sequencing Primer
(F):5'- GCTGGGACAACCTTCTCTAACATG -3'
(R):5'- GGCATCATAAGCTCTTAAAGGC -3'

Posted On

2015-11-11