Incidental Mutation 'R0179:Synj1'
ID 23072
Institutional Source Beutler Lab
Gene Symbol Synj1
Ensembl Gene ENSMUSG00000022973
Gene Name synaptojanin 1
Synonyms A930006D20Rik
MMRRC Submission 038447-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0179 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 16
Chromosomal Location 90732980-90808196 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 90761519 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 649 (K649R)
Ref Sequence ENSEMBL: ENSMUSP00000113308 (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: K623R
SMART Domains Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: K623R

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 possibly damaging
Transcript: ENSMUST00000121759
AA Change: K649R

PolyPhen 2 Score 0.804 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: K649R

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: ENSMUST00000130813
AA Change: K604R

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973
AA Change: K604R

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 benign
Transcript: ENSMUST00000170853
AA Change: K609R

PolyPhen 2 Score 0.118 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: K609R

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: ENSMUST00000231472
Meta Mutation Damage Score 0.1179 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.8%
  • 20x: 94.1%
Validation Efficiency 98% (81/83)
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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts1 C T 16: 85,592,353 (GRCm39) S948N probably benign Het
Adck1 A T 12: 88,425,942 (GRCm39) M457L possibly damaging Het
Adprm A T 11: 66,929,051 (GRCm39) H313Q possibly damaging Het
Adss1 T C 12: 112,598,703 (GRCm39) I104T probably benign Het
Agxt2 A C 15: 10,399,134 (GRCm39) Q435P possibly damaging Het
Amotl1 G A 9: 14,460,069 (GRCm39) A890V probably benign Het
Ankrd50 A G 3: 38,509,463 (GRCm39) V968A possibly damaging Het
Brf2 T C 8: 27,615,896 (GRCm39) D163G possibly damaging Het
Cd226 C A 18: 89,225,263 (GRCm39) N53K probably benign Het
Cdc42ep2 T C 19: 5,968,636 (GRCm39) D23G probably benign Het
Cdc7 T C 5: 107,112,905 (GRCm39) S8P probably benign Het
Cdh8 C T 8: 99,838,344 (GRCm39) E499K possibly damaging Het
Chd7 T A 4: 8,862,516 (GRCm39) F2534L probably benign Het
Ckb T C 12: 111,636,610 (GRCm39) T255A probably benign Het
Cntnap5c G T 17: 58,076,620 (GRCm39) W19L probably benign Het
Cntrl A G 2: 35,057,871 (GRCm39) E1854G probably benign Het
Colec12 C T 18: 9,858,921 (GRCm39) P568L unknown Het
Cop1 A G 1: 159,077,636 (GRCm39) D157G probably benign Het
Csf2rb A C 15: 78,220,572 (GRCm39) Q38P possibly damaging Het
Ctla2b T C 13: 61,044,107 (GRCm39) D52G possibly damaging Het
Dcaf7 A T 11: 105,942,623 (GRCm39) D190V probably damaging Het
Depdc5 T A 5: 33,058,918 (GRCm39) probably benign Het
Dgkq A G 5: 108,806,066 (GRCm39) probably benign Het
Dhrs2 A G 14: 55,477,933 (GRCm39) T222A probably damaging Het
Dock1 G A 7: 134,700,566 (GRCm39) D1109N probably damaging Het
E4f1 G C 17: 24,670,411 (GRCm39) T92S possibly damaging Het
Ep400 A T 5: 110,816,515 (GRCm39) S2669T probably damaging Het
Eprs1 T G 1: 185,145,744 (GRCm39) D1184E probably benign Het
Fpr-rs4 A T 17: 18,242,289 (GRCm39) K99* probably null Het
Fzr1 A T 10: 81,204,904 (GRCm39) probably benign Het
Gcc2 C T 10: 58,112,472 (GRCm39) R1001C probably benign Het
Gm4884 A G 7: 40,693,252 (GRCm39) D407G probably benign Het
Golga4 A T 9: 118,389,808 (GRCm39) probably null Het
Gp2 T G 7: 119,051,540 (GRCm39) D225A possibly damaging Het
Gramd1a T A 7: 30,841,843 (GRCm39) T120S probably damaging Het
Hbb-bh2 T A 7: 103,488,434 (GRCm39) N121I probably benign Het
Htr6 A T 4: 138,789,437 (GRCm39) L276Q probably damaging Het
Itga9 A T 9: 118,490,454 (GRCm39) I262F probably benign Het
Lamc3 A G 2: 31,805,096 (GRCm39) probably benign Het
Large1 T C 8: 73,825,474 (GRCm39) N200S probably benign Het
Lct C T 1: 128,255,422 (GRCm39) V207I probably benign Het
Marf1 C A 16: 13,969,040 (GRCm39) L144F probably damaging Het
Morc2b A T 17: 33,355,956 (GRCm39) Y605* probably null Het
Mtus1 G T 8: 41,455,398 (GRCm39) L87I possibly damaging Het
Muc2 A G 7: 141,302,708 (GRCm39) Y17C probably damaging Het
Myf5 T C 10: 107,321,779 (GRCm39) D5G possibly damaging Het
Nasp C T 4: 116,459,354 (GRCm39) V375M probably damaging Het
Nr1h2 A T 7: 44,201,689 (GRCm39) probably null Het
Nrg2 T C 18: 36,155,468 (GRCm39) Q447R probably benign Het
Ntn5 G A 7: 45,335,737 (GRCm39) G56D probably damaging Het
Oasl2 A G 5: 115,048,973 (GRCm39) R138G probably benign Het
Or4c29 A T 2: 88,740,237 (GRCm39) C167S possibly damaging Het
Or5b124 T A 19: 13,610,504 (GRCm39) F10I probably damaging Het
Or9k7 T C 10: 130,046,207 (GRCm39) Y264C probably damaging Het
Pcdhb5 G A 18: 37,455,612 (GRCm39) G664D probably damaging Het
Ppp1r15a T C 7: 45,174,424 (GRCm39) E128G probably damaging Het
Prpf19 T C 19: 10,875,172 (GRCm39) probably benign Het
Ptpn3 T A 4: 57,270,118 (GRCm39) T15S probably benign Het
R3hdm2 G A 10: 127,330,975 (GRCm39) C818Y probably damaging Het
Rad51d A G 11: 82,780,824 (GRCm39) V39A possibly damaging Het
Rptor A T 11: 119,763,193 (GRCm39) T926S probably benign Het
Rwdd4a G A 8: 47,995,742 (GRCm39) D41N probably damaging Het
Sephs1 A G 2: 4,904,371 (GRCm39) T250A probably benign Het
Spata31g1 T C 4: 42,972,214 (GRCm39) S516P probably benign Het
Ssbp3 T C 4: 106,903,585 (GRCm39) S334P probably damaging Het
Suco A G 1: 161,703,874 (GRCm39) probably benign Het
Tdp2 C T 13: 25,024,431 (GRCm39) H243Y possibly damaging Het
Tinag A G 9: 76,904,164 (GRCm39) probably benign Het
Trerf1 T C 17: 47,627,588 (GRCm39) noncoding transcript Het
Trip10 T C 17: 57,569,349 (GRCm39) probably benign Het
Tsen54 A T 11: 115,712,856 (GRCm39) S131C probably damaging Het
Unc5c A T 3: 141,523,828 (GRCm39) R794* probably null Het
Vmn2r59 A T 7: 41,696,432 (GRCm39) Y103* probably null Het
Washc5 A G 15: 59,224,379 (GRCm39) V460A probably benign Het
Wdr87-ps A G 7: 29,235,365 (GRCm39) noncoding transcript Het
Whamm A G 7: 81,243,763 (GRCm39) T358A probably benign Het
Xlr4b C T X: 72,262,277 (GRCm39) probably benign Het
Zbbx C T 3: 74,992,869 (GRCm39) probably benign Het
Zdhhc23 G A 16: 43,794,066 (GRCm39) P203S probably benign Het
Zfp27 T A 7: 29,595,850 (GRCm39) E38D 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
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
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'- AATGGACGAGATGGCATCGCAC -3'
(R):5'- AAGTTTATCTGAGTTGCTCACCTCACG -3'

Sequencing Primer
(F):5'- TGGCATCGCACACACTAGG -3'
(R):5'- gtatgtggaggtcagaggatag -3'
Posted On 2013-04-16