Incidental Mutation 'R6005:Synj1'
ID 479449
Institutional Source Beutler Lab
Gene Symbol Synj1
Ensembl Gene ENSMUSG00000022973
Gene Name synaptojanin 1
Synonyms A930006D20Rik
MMRRC Submission 044425-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6005 (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 90766174 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 541 (N541K)
Ref Sequence ENSEMBL: ENSMUSP00000128997 (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: N555K
SMART Domains Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: N555K

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 damaging
Transcript: ENSMUST00000121759
AA Change: N581K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: N581K

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 damaging
Transcript: ENSMUST00000130813
AA Change: N536K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973
AA Change: N536K

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000170853
AA Change: N541K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: N541K

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 damaging
Transcript: ENSMUST00000231472
AA Change: N20K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.2%
  • 20x: 90.9%
Validation Efficiency 99% (79/80)
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
7530416G11Rik A T 15: 85,378,310 (GRCm39) I111N unknown Het
Adgb C T 10: 10,271,096 (GRCm39) R849H probably damaging Het
Ahnak T C 19: 8,992,525 (GRCm39) V4603A possibly damaging Het
Ank1 A G 8: 23,622,218 (GRCm39) D1589G probably damaging Het
Ankrd2 A G 19: 42,028,554 (GRCm39) D70G probably damaging Het
Arid2 T C 15: 96,268,853 (GRCm39) S989P probably benign Het
Bbs1 A T 19: 4,953,823 (GRCm39) Y113* probably null Het
Bfsp2 T G 9: 103,325,749 (GRCm39) K298T probably damaging Het
Bpi G A 2: 158,104,400 (GRCm39) V168I possibly damaging Het
Cacna2d1 T C 5: 16,566,819 (GRCm39) S921P probably damaging Het
Clec4d A C 6: 123,244,118 (GRCm39) T76P probably damaging Het
Coq8b C T 7: 26,956,750 (GRCm39) Q468* probably null Het
Dennd6b T C 15: 89,072,371 (GRCm39) E248G possibly damaging Het
Ednra A G 8: 78,401,556 (GRCm39) S245P possibly damaging Het
Epb41l4a C T 18: 33,961,196 (GRCm39) C446Y probably benign Het
Fam221a A G 6: 49,344,756 (GRCm39) probably benign Het
Fam229a T C 4: 129,385,296 (GRCm39) S76P probably benign Het
Fryl C T 5: 73,240,638 (GRCm39) D1321N probably damaging Het
Gata3os T C 2: 9,887,638 (GRCm39) probably benign Het
Gli2 C T 1: 118,769,794 (GRCm39) R586H probably damaging Het
Gm94 C T 18: 43,925,862 (GRCm39) A16T possibly damaging Het
Gorasp2 T C 2: 70,521,095 (GRCm39) V355A probably benign Het
Grid1 C A 14: 35,045,369 (GRCm39) T404N probably damaging Het
Gtf2i C A 5: 134,284,812 (GRCm39) E475* probably null Het
Gucy1a2 T C 9: 3,865,518 (GRCm39) probably null Het
Hs3st5 T A 10: 36,708,924 (GRCm39) I153N probably damaging Het
Il11ra1 T C 4: 41,763,887 (GRCm39) probably null Het
Ireb2 G A 9: 54,816,089 (GRCm39) G887S probably damaging Het
Kdsr T C 1: 106,662,311 (GRCm39) E248G probably benign Het
Lemd2 C G 17: 27,409,759 (GRCm39) R464P probably damaging Het
Lrrfip1 T C 1: 91,042,333 (GRCm39) V246A probably damaging Het
Macf1 T A 4: 123,368,068 (GRCm39) D2231V possibly damaging Het
Map2k5 C T 9: 63,188,301 (GRCm39) D283N probably damaging Het
Mfsd5 A G 15: 102,189,927 (GRCm39) D433G possibly damaging Het
Mir700 C A 4: 135,139,618 (GRCm39) probably null Het
Mroh9 A T 1: 162,903,246 (GRCm39) F52L probably damaging Het
Mtrfr G T 5: 124,478,837 (GRCm39) E153* probably null Het
Mycbp2 A C 14: 103,394,159 (GRCm39) S2691A probably benign Het
Myorg T A 4: 41,498,895 (GRCm39) H245L probably benign Het
Nktr T A 9: 121,577,460 (GRCm39) probably benign Het
Obsl1 C A 1: 75,468,859 (GRCm39) probably null Het
Or10ag60 A T 2: 87,438,424 (GRCm39) I231F probably damaging Het
Or52r1b A T 7: 102,690,853 (GRCm39) I51F probably damaging Het
Or5aq7 A G 2: 86,938,407 (GRCm39) V108A probably benign Het
Or7g35 C T 9: 19,496,181 (GRCm39) T116I probably benign Het
Or8c11 T C 9: 38,289,605 (GRCm39) S137P probably damaging Het
Pcdhb22 T A 18: 37,652,789 (GRCm39) I162N possibly damaging Het
Pde1c A T 6: 56,456,187 (GRCm39) probably null Het
Pds5b A G 5: 150,693,241 (GRCm39) probably null Het
Pkd1l1 A C 11: 8,807,113 (GRCm39) W1568G probably damaging Het
Polr3c A T 3: 96,626,784 (GRCm39) M258K possibly damaging Het
Pramel23 T A 4: 143,425,002 (GRCm39) H147L probably benign Het
Prss12 A T 3: 123,276,417 (GRCm39) I349F probably benign Het
Ptpn21 A G 12: 98,644,811 (GRCm39) *1177Q probably null Het
Rgs22 T A 15: 36,010,713 (GRCm39) K1125M probably benign Het
Rnf182 A G 13: 43,821,511 (GRCm39) K21E probably damaging Het
Rpl6 G A 5: 121,343,577 (GRCm39) probably benign Het
Samsn1 C T 16: 75,670,402 (GRCm39) V234I probably benign Het
Scrib A G 15: 75,929,600 (GRCm39) I1089T probably damaging Het
Sec31a T C 5: 100,511,737 (GRCm39) T1092A probably damaging Het
Sh3bp2 G T 5: 34,719,809 (GRCm39) R606L possibly damaging Het
Sipa1 A G 19: 5,706,229 (GRCm39) V367A probably damaging Het
Slc25a44 C T 3: 88,320,153 (GRCm39) E269K probably damaging Het
Slc44a4 T A 17: 35,142,430 (GRCm39) M353K possibly damaging Het
Sorcs2 A G 5: 36,176,728 (GRCm39) S1142P probably damaging Het
Sptbn4 A G 7: 27,118,024 (GRCm39) F352L probably damaging Het
Tas2r113 G A 6: 132,870,659 (GRCm39) R229K probably benign Het
Tcaf3 A T 6: 42,566,905 (GRCm39) I728K probably benign Het
Tcea1 A G 1: 4,960,996 (GRCm39) E167G probably benign Het
Timeless G A 10: 128,080,069 (GRCm39) R406H probably damaging Het
Traf6 C T 2: 101,527,029 (GRCm39) R260* probably null Het
Traj31 C T 14: 54,425,388 (GRCm39) probably benign Het
Ttn A T 2: 76,599,907 (GRCm39) V19089D probably damaging Het
Unc80 C T 1: 66,666,416 (GRCm39) S1868L possibly damaging Het
Wdr38 A T 2: 38,891,333 (GRCm39) I287F possibly damaging Het
Wnt2 G A 6: 18,030,322 (GRCm39) probably benign Het
Wnt5b G A 6: 119,410,615 (GRCm39) P288L probably benign Het
Xkr5 G T 8: 18,984,521 (GRCm39) N174K probably benign Het
Zbtb6 C T 2: 37,318,977 (GRCm39) R317Q probably damaging Het
Zcchc7 AGGGG AGGG 4: 44,931,218 (GRCm39) probably null Het
Zfp647 G A 15: 76,796,285 (GRCm39) P125L probably 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
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'- GCCGAGTTTCTGTTCTAAATTAGTG -3'
(R):5'- CTTGGCATTCAAGGCTGATCTC -3'

Sequencing Primer
(F):5'- TGAAGTGTCACATTGCAGTCAG -3'
(R):5'- AAGGCTGATCTCTCCCTTGTG -3'
Posted On 2017-06-26