Incidental Mutation 'R0486:Synj1'
ID 42307
Institutional Source Beutler Lab
Gene Symbol Synj1
Ensembl Gene ENSMUSG00000022973
Gene Name synaptojanin 1
Synonyms A930006D20Rik
MMRRC Submission 038685-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0486 (G1)
Quality Score 225
Status Validated
Chromosome 16
Chromosomal Location 90732980-90808196 bp(-) (GRCm39)
Type of Mutation utr 3 prime
DNA Base Change (assembly) T to C at 90735151 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000128997 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023694] [ENSMUST00000121759] [ENSMUST00000125519] [ENSMUST00000129743] [ENSMUST00000170853] [ENSMUST00000149833] [ENSMUST00000142340]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000023694
SMART Domains Protein: ENSMUSP00000023694
Gene: ENSMUSG00000022972

DomainStartEndE-ValueType
Pfam:DUF2870 189 285 4.7e-47 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118390
SMART Domains Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973

DomainStartEndE-ValueType
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 unknown
Transcript: ENSMUST00000121759
AA Change: T1601A
SMART Domains Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: T1601A

DomainStartEndE-ValueType
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: ENSMUST00000125519
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129041
Predicted Effect probably benign
Transcript: ENSMUST00000129743
SMART Domains Protein: ENSMUSP00000123231
Gene: ENSMUSG00000022973

DomainStartEndE-ValueType
low complexity region 69 101 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131583
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232326
Predicted Effect probably benign
Transcript: ENSMUST00000170853
SMART Domains Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973

DomainStartEndE-ValueType
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: ENSMUST00000149833
SMART Domains Protein: ENSMUSP00000123417
Gene: ENSMUSG00000022972

DomainStartEndE-ValueType
Pfam:DUF2870 171 198 5.8e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000142340
Predicted Effect probably benign
Transcript: ENSMUST00000154276
SMART Domains Protein: ENSMUSP00000122675
Gene: ENSMUSG00000022973

DomainStartEndE-ValueType
low complexity region 2 32 N/A INTRINSIC
low complexity region 54 73 N/A INTRINSIC
low complexity region 154 187 N/A INTRINSIC
Meta Mutation Damage Score 0.0720 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.9%
Validation Efficiency 98% (65/66)
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aco1 T C 4: 40,177,783 (GRCm39) L268P probably damaging Het
Adam22 A T 5: 8,380,048 (GRCm39) H83Q probably damaging Het
Anln T C 9: 22,264,122 (GRCm39) D886G probably benign Het
Arhgef11 T A 3: 87,596,159 (GRCm39) probably null Het
Ark2c T A 18: 77,571,950 (GRCm39) Q91L probably damaging Het
Arl8b A T 6: 108,792,287 (GRCm39) D116V possibly damaging Het
BC051665 C T 13: 60,931,859 (GRCm39) G180D probably damaging Het
Bloc1s2 A G 19: 44,131,589 (GRCm39) probably benign Het
Ccdc185 T G 1: 182,575,424 (GRCm39) S422R possibly damaging Het
Cd101 T C 3: 100,915,408 (GRCm39) K720E possibly damaging Het
Cdh23 C A 10: 60,222,725 (GRCm39) A1236S probably damaging Het
Chd1 G A 17: 15,954,604 (GRCm39) A491T probably damaging Het
Chdh T C 14: 29,754,815 (GRCm39) V275A possibly damaging Het
Cmtm2b A T 8: 105,057,047 (GRCm39) I136F probably damaging Het
Cps1 T C 1: 67,204,551 (GRCm39) V457A probably damaging Het
Cwf19l1 A G 19: 44,103,129 (GRCm39) V362A probably benign Het
Cyp4f17 T C 17: 32,743,797 (GRCm39) probably benign Het
Cyp4f18 C A 8: 72,749,861 (GRCm39) V263L probably benign Het
Dclre1a A G 19: 56,529,922 (GRCm39) probably benign Het
Dpp6 T C 5: 27,866,640 (GRCm39) I446T probably benign Het
F11r T C 1: 171,288,156 (GRCm39) W61R probably damaging Het
Fam120b C T 17: 15,646,550 (GRCm39) probably benign Het
Fastkd2 T C 1: 63,791,499 (GRCm39) V669A possibly damaging Het
Foxg1 T C 12: 49,431,314 (GRCm39) probably benign Het
Foxo3 A G 10: 42,073,477 (GRCm39) Y347H probably damaging Het
G3bp1 T C 11: 55,389,452 (GRCm39) F383L probably damaging Het
Gbp7 C A 3: 142,252,078 (GRCm39) probably benign Het
Glipr1 T C 10: 111,832,754 (GRCm39) probably benign Het
Gm11555 A G 11: 99,540,986 (GRCm39) S8P unknown Het
H6pd G A 4: 150,067,393 (GRCm39) probably benign Het
Haus8 C T 8: 71,709,182 (GRCm39) M75I probably benign Het
Haus8 C A 8: 71,709,181 (GRCm39) G76W probably damaging Het
Kcnj13 C A 1: 87,314,752 (GRCm39) V157L probably damaging Het
Kcnt2 T A 1: 140,437,218 (GRCm39) C550* probably null Het
Kdm5d A G Y: 927,107 (GRCm39) N615S probably damaging Het
Naip2 A C 13: 100,298,290 (GRCm39) I582S probably benign Het
Ncapd2 G A 6: 125,160,990 (GRCm39) R292* probably null Het
Ngef T A 1: 87,406,848 (GRCm39) N640I probably damaging Het
Nhlrc3 T C 3: 53,359,858 (GRCm39) Y335C probably damaging Het
Nipbl A T 15: 8,368,354 (GRCm39) probably benign Het
Nop2 A G 6: 125,117,636 (GRCm39) K434R probably null Het
Nr4a3 T C 4: 48,056,525 (GRCm39) probably benign Het
Or8b35 A G 9: 37,903,998 (GRCm39) N70S possibly damaging Het
Piezo2 A C 18: 63,162,132 (GRCm39) I2233R probably damaging Het
Prag1 A T 8: 36,613,787 (GRCm39) E1113V probably damaging Het
Prpsap2 A G 11: 61,631,826 (GRCm39) I177T possibly damaging Het
Psmd1 T A 1: 86,022,012 (GRCm39) N611K probably damaging Het
Ptpn7 C T 1: 135,065,096 (GRCm39) T168I probably damaging Het
Pus1 A T 5: 110,927,596 (GRCm39) V53E probably damaging Het
Rgs22 A G 15: 36,093,028 (GRCm39) M415T probably damaging Het
Rnf17 C T 14: 56,751,632 (GRCm39) T1490M probably benign Het
Rnf20 C A 4: 49,645,907 (GRCm39) L332I possibly damaging Het
Snrnp40 C G 4: 130,271,836 (GRCm39) probably null Het
Spam1 A T 6: 24,796,394 (GRCm39) Q115L probably damaging Het
Syce1l A T 8: 114,381,395 (GRCm39) probably null Het
Tas2r126 A T 6: 42,412,225 (GRCm39) I253F probably benign Het
Tecpr2 G A 12: 110,862,803 (GRCm39) V72I probably benign Het
Tfap2a G T 13: 40,882,170 (GRCm39) P45Q probably damaging Het
Trip12 C A 1: 84,738,805 (GRCm39) G714* probably null Het
Wdr31 A G 4: 62,372,130 (GRCm39) S330P probably damaging Het
Wdr64 T C 1: 175,622,769 (GRCm39) probably benign Het
Yes1 T A 5: 32,812,926 (GRCm39) Y343* probably null Het
Other mutations in Synj1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- ATCCTCAACAGCACAATGGGCTGC -3'
(R):5'- CGCGCCAGCTTCATTTGATGATGAC -3'

Sequencing Primer
(F):5'- GATATACACAAATTCCAGCTTTCTCC -3'
(R):5'- TCATTTGATGATGACTGGAGTAAAGG -3'
Posted On 2013-05-23