Incidental Mutation 'R9052:Synj1'
ID 688480
Institutional Source Beutler Lab
Gene Symbol Synj1
Ensembl Gene ENSMUSG00000022973
Gene Name synaptojanin 1
Synonyms A930006D20Rik
MMRRC Submission 068878-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9052 (G1)
Quality Score 225.009
Status Validated
Chromosome 16
Chromosomal Location 90732980-90808196 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 90735728 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 1408 (S1408R)
Ref Sequence ENSEMBL: ENSMUSP00000113308 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023694] [ENSMUST00000121759] [ENSMUST00000125519] [ENSMUST00000129743] [ENSMUST00000142340] [ENSMUST00000149833] [ENSMUST00000170853]
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 probably benign
Transcript: ENSMUST00000121759
AA Change: S1408R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: S1408R

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 probably benign
Transcript: ENSMUST00000129743
SMART Domains Protein: ENSMUSP00000123231
Gene: ENSMUSG00000022973

DomainStartEndE-ValueType
low complexity region 69 101 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000142340
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: 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
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.6%
Validation Efficiency 99% (69/70)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110059G10Rik T C 9: 122,778,031 (GRCm39) E71G probably damaging Het
2610021A01Rik G T 7: 41,275,449 (GRCm39) G384V probably benign Het
4931406B18Rik T A 7: 43,147,631 (GRCm39) R247* probably null Het
Abca4 G T 3: 121,940,908 (GRCm39) V1576F possibly damaging Het
Acsl6 A T 11: 54,232,615 (GRCm39) T489S possibly damaging Het
Adcy8 C T 15: 64,792,764 (GRCm39) R64H probably benign Het
Atad2b C A 12: 5,015,982 (GRCm39) F569L probably damaging Het
Atp2c1 A T 9: 105,330,032 (GRCm39) I266N probably damaging Het
Atp8a1 A G 5: 67,936,301 (GRCm39) probably null Het
Coch T C 12: 51,640,408 (GRCm39) M1T probably null Het
Col5a3 C A 9: 20,710,733 (GRCm39) R537L unknown Het
Crb1 C T 1: 139,171,161 (GRCm39) R743Q possibly damaging Het
Crybg2 T C 4: 133,803,035 (GRCm39) F889L probably damaging Het
Cyp4f15 C T 17: 32,911,589 (GRCm39) T157I probably damaging Het
D630045J12Rik G T 6: 38,154,544 (GRCm39) Q1212K probably damaging Het
Dennd1a A G 2: 37,911,463 (GRCm39) Y175H probably damaging Het
Dhcr7 C A 7: 143,395,060 (GRCm39) T192K possibly damaging Het
Dlg1 T A 16: 31,656,942 (GRCm39) I612N probably damaging Het
Dmpk G A 7: 18,821,614 (GRCm39) V291M probably damaging Het
Dnajc6 T C 4: 101,496,617 (GRCm39) V928A probably damaging Het
Dst A G 1: 34,206,045 (GRCm39) Y859C probably damaging Het
Dst C T 1: 34,236,411 (GRCm39) Q1592* probably null Het
Gm10226 T A 17: 21,910,959 (GRCm39) C65S possibly damaging Het
Helz2 T C 2: 180,881,968 (GRCm39) K275R possibly damaging Het
Hltf A G 3: 20,152,246 (GRCm39) T581A probably damaging Het
Ighv1-24 C T 12: 114,736,555 (GRCm39) C115Y probably damaging Het
Il18 C T 9: 50,489,090 (GRCm39) L40F possibly damaging Het
Isg20 A G 7: 78,566,390 (GRCm39) D113G probably damaging Het
Itgb3 A T 11: 104,524,413 (GRCm39) D183V probably damaging Het
Kif12 C T 4: 63,090,068 (GRCm39) V28M probably damaging Het
Manbal T C 2: 157,221,107 (GRCm39) L28P probably damaging Het
Masp1 T A 16: 23,339,350 (GRCm39) probably benign Het
Mfap5 A G 6: 122,501,463 (GRCm39) T72A probably benign Het
Mier2 G A 10: 79,384,274 (GRCm39) R166W probably damaging Het
Mrps5 G A 2: 127,433,876 (GRCm39) probably benign Het
Ms4a1 T A 19: 11,233,954 (GRCm39) T101S probably benign Het
Myo3b A G 2: 70,062,747 (GRCm39) M344V probably benign Het
Naaladl1 T G 19: 6,158,716 (GRCm39) F283V probably benign Het
Nacc1 A C 8: 85,403,377 (GRCm39) V166G probably damaging Het
Nwd2 A T 5: 63,961,773 (GRCm39) R452S probably damaging Het
Or1n1b T C 2: 36,780,105 (GRCm39) T252A probably damaging Het
Or1x6 G A 11: 50,938,938 (GRCm39) M1I probably null Het
Or5k16 T C 16: 58,736,561 (GRCm39) T148A probably benign Het
Or6c214 C G 10: 129,591,094 (GRCm39) C75S possibly damaging Het
Pik3cg T C 12: 32,245,708 (GRCm39) I847V possibly damaging Het
Plcz1 G A 6: 139,968,905 (GRCm39) H178Y probably damaging Het
Prkdc T A 16: 15,508,160 (GRCm39) M937K probably benign Het
Prr14l A T 5: 32,987,478 (GRCm39) C672* probably null Het
Rasl11a C A 5: 146,782,107 (GRCm39) D27E probably benign Het
Rbm27 T C 18: 42,465,893 (GRCm39) S860P probably damaging Het
Rfxap G A 3: 54,715,155 (GRCm39) probably benign Het
Rhbdf2 A C 11: 116,494,758 (GRCm39) L306R probably benign Het
Rigi C A 4: 40,208,459 (GRCm39) V826L probably benign Het
Rnf123 A T 9: 107,936,930 (GRCm39) V875E probably damaging Het
Sh3bp2 A G 5: 34,709,164 (GRCm39) probably benign Het
Slc7a9 A G 7: 35,153,017 (GRCm39) K145R probably benign Het
Slco5a1 A T 1: 13,060,397 (GRCm39) V108E possibly damaging Het
Stat2 A G 10: 128,117,538 (GRCm39) E352G probably damaging Het
Tent5c A T 3: 100,380,618 (GRCm39) I46K probably benign Het
Tgs1 T A 4: 3,585,166 (GRCm39) M102K probably benign Het
Tnfrsf11a G A 1: 105,754,854 (GRCm39) A309T possibly damaging Het
Ttc23 C A 7: 67,342,687 (GRCm39) C268* probably null Het
Uhrf2 T C 19: 30,070,236 (GRCm39) F795S probably damaging Het
Urgcp A G 11: 5,673,153 (GRCm39) W41R probably damaging Het
Uso1 G T 5: 92,328,422 (GRCm39) V340F probably damaging Het
Vta1 A C 10: 14,551,692 (GRCm39) I169R probably benign Het
Zfp317 A G 9: 19,556,568 (GRCm39) I59V probably benign Het
Zfp799 G A 17: 33,039,786 (GRCm39) T160I probably benign Het
Zfp955a G T 17: 33,461,279 (GRCm39) H284Q possibly damaging 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
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
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'- TCGTGTCATGACTGAGAGGC -3'
(R):5'- GTGTCAAACAAGAGCCAACATTG -3'

Sequencing Primer
(F):5'- GAGCCAAGAAGTTGCCTCTGATTC -3'
(R):5'- GAAGAGTGACCCATTTGAAGATCTC -3'
Posted On 2021-11-19