Incidental Mutation 'R9732:Synj1'
ID 731507
Institutional Source Beutler Lab
Gene Symbol Synj1
Ensembl Gene ENSMUSG00000022973
Gene Name synaptojanin 1
Synonyms A930006D20Rik
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9732 (G1)
Quality Score 225.009
Status Not validated
Chromosome 16
Chromosomal Location 90732980-90808196 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 90761414 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 684 (P684L)
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
SMART Domains Protein: ENSMUSP00000113518
Gene: ENSMUSG00000022973
AA Change: P658L

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: P684L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113308
Gene: ENSMUSG00000022973
AA Change: P684L

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: P639L

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000119712
Gene: ENSMUSG00000022973
AA Change: P639L

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 possibly damaging
Transcript: ENSMUST00000170853
AA Change: P644L

PolyPhen 2 Score 0.912 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000128997
Gene: ENSMUSG00000022973
AA Change: P644L

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.8%
  • 10x: 99.5%
  • 20x: 99.0%
Validation Efficiency
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agrn A T 4: 156,258,446 (GRCm39) S1007T probably benign Het
Akap10 A T 11: 61,787,545 (GRCm39) C466S probably damaging Het
Apol9b C T 15: 77,619,566 (GRCm39) P121S possibly damaging Het
Atr T A 9: 95,743,438 (GRCm39) Y26N probably damaging Het
Cadm2 G A 16: 66,528,297 (GRCm39) T346I probably benign Het
Capn7 T C 14: 31,090,031 (GRCm39) I628T probably damaging Het
Cfap43 A G 19: 47,775,446 (GRCm39) S609P probably damaging Het
Chst2 C T 9: 95,287,951 (GRCm39) G132S probably benign Het
Clip2 C T 5: 134,533,616 (GRCm39) R487Q probably benign Het
Coq10a A G 10: 128,199,516 (GRCm39) F253L probably benign Het
Cyp2t4 C T 7: 26,854,657 (GRCm39) P46S probably damaging Het
Ddx54 T C 5: 120,763,911 (GRCm39) probably null Het
Dip2a T A 10: 76,110,077 (GRCm39) I1180L probably benign Het
Dpp8 G T 9: 64,970,862 (GRCm39) probably null Het
Efr3a T A 15: 65,720,139 (GRCm39) N378K probably benign Het
Etl4 C T 2: 20,748,373 (GRCm39) T237I probably damaging Het
Exo1 T A 1: 175,727,065 (GRCm39) S459T probably benign Het
Fam81b G A 13: 76,399,985 (GRCm39) T91I probably benign Het
Fry A G 5: 150,328,758 (GRCm39) E1297G probably benign Het
Gm11110 G A 17: 57,410,382 (GRCm39) L39F unknown Het
Gm3233 G T 10: 77,595,147 (GRCm39) Q124K unknown Het
Gm7145 C G 1: 117,913,839 (GRCm39) H240Q probably benign Het
Gnrh1 G T 14: 67,985,316 (GRCm39) R67L possibly damaging Het
Grip2 T A 6: 91,761,686 (GRCm39) E236V probably damaging Het
H3c10 A T 13: 21,902,186 (GRCm39) I120F probably benign Het
Hectd4 G T 5: 121,392,254 (GRCm39) E173* probably null Het
Hgf T A 5: 16,820,748 (GRCm39) L632I probably damaging Het
Igsf11 T C 16: 38,843,652 (GRCm39) V255A probably benign Het
Jmjd4 G T 11: 59,341,339 (GRCm39) probably null Het
Khdrbs3 C A 15: 68,885,212 (GRCm39) N71K probably damaging Het
Kif20b A G 19: 34,930,353 (GRCm39) D1286G probably benign Het
Lpin3 T A 2: 160,734,196 (GRCm39) L27Q probably damaging Het
Macroh2a1 G C 13: 56,243,976 (GRCm39) F183L probably benign Het
Mcm5 C T 8: 75,844,168 (GRCm39) S313F probably benign Het
Mipep T A 14: 61,033,637 (GRCm39) F184I probably damaging Het
Mst1 A T 9: 107,959,425 (GRCm39) D237V possibly damaging Het
Mycbp2 T C 14: 103,448,749 (GRCm39) D1803G probably damaging Het
Ncoa6 T G 2: 155,244,636 (GRCm39) K1978T probably damaging Het
Nkain4 G A 2: 180,585,901 (GRCm39) T54I probably damaging Het
Olig3 G A 10: 19,233,151 (GRCm39) A259T probably benign Het
Or5w14 T C 2: 87,541,489 (GRCm39) T254A possibly damaging Het
Pacs1 A G 19: 5,184,997 (GRCm39) W943R probably damaging Het
Pkp4 T A 2: 59,138,797 (GRCm39) L349Q possibly damaging Het
Polh A T 17: 46,498,997 (GRCm39) H239Q probably benign Het
Ptprq G C 10: 107,412,767 (GRCm39) C1777W probably damaging Het
Rhod A T 19: 4,476,740 (GRCm39) V127E probably damaging Het
Rnf6 A G 5: 146,152,931 (GRCm39) S84P probably benign Het
Rundc3b T C 5: 8,562,406 (GRCm39) T321A probably damaging Het
Rxfp2 G A 5: 149,993,767 (GRCm39) A620T probably damaging Het
Sacm1l A G 9: 123,381,863 (GRCm39) E155G probably benign Het
Saxo5 C T 8: 3,526,167 (GRCm39) H107Y possibly damaging Het
Sdad1 A T 5: 92,438,942 (GRCm39) D471E probably benign Het
Sema6a T A 18: 47,381,925 (GRCm39) N874I probably damaging Het
Serinc4 C A 2: 121,283,631 (GRCm39) W283L possibly damaging Het
Simc1 GCAGTCACTAAGAAGTGTAATGCAGTCATCAGGAGGTGTGACACAGTCACTAAGAAGTGTGATGCAGTCACCAGGAGGTGTGA GCAGTCACTAAGAAGTGTGATGCAGTCACCAGGAGGTGTGA 13: 54,673,177 (GRCm39) probably benign Het
Slc24a3 A T 2: 145,458,591 (GRCm39) S524C probably damaging Het
Slc4a10 T G 2: 62,135,086 (GRCm39) S1042R probably damaging Het
Smg7 A T 1: 152,736,212 (GRCm39) V190D probably damaging Het
Sub1 T A 15: 11,986,650 (GRCm39) I66F possibly damaging Het
Svop G A 5: 114,201,142 (GRCm39) P109S probably damaging Het
Synm A G 7: 67,385,652 (GRCm39) V670A probably damaging Het
Tep1 T C 14: 51,088,162 (GRCm39) I792V probably benign Het
Tex22 A G 12: 113,052,196 (GRCm39) T85A possibly damaging Het
Tmem151a C T 19: 5,131,937 (GRCm39) S423N probably damaging Het
Tnks1bp1 T A 2: 84,889,727 (GRCm39) W685R probably damaging Het
Top3a A G 11: 60,640,391 (GRCm39) F436L probably benign Het
Trim55 A T 3: 19,716,039 (GRCm39) I200F probably damaging Het
Trpv6 T A 6: 41,603,862 (GRCm39) R186* probably null Het
Ttc6 G A 12: 57,775,335 (GRCm39) C1677Y probably benign Het
Ttn C T 2: 76,769,206 (GRCm39) V2831I unknown Het
Tyrp1 T A 4: 80,758,930 (GRCm39) S268T possibly damaging Het
Unc5d C T 8: 29,381,319 (GRCm39) probably null Het
Usb1 G T 8: 96,065,375 (GRCm39) V129L probably damaging Het
Usp22 G A 11: 61,051,437 (GRCm39) T302M probably damaging Het
Vmn1r210 C A 13: 23,011,379 (GRCm39) L302F possibly damaging Het
Zfp689 C A 7: 127,044,283 (GRCm39) E116* 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
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
Z1176:Synj1 UTSW 16 90,784,228 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGAGCATCCGAATTGCAACG -3'
(R):5'- GCAGCTTGCATGAAAATGTTC -3'

Sequencing Primer
(F):5'- AATTGCAACGGCGCCCTTG -3'
(R):5'- TTAAGCAATCAGATGTATAAAGGGC -3'
Posted On 2022-11-14