Incidental Mutation 'R0530:Synj2'
ID 49124
Institutional Source Beutler Lab
Gene Symbol Synj2
Ensembl Gene ENSMUSG00000023805
Gene Name synaptojanin 2
Synonyms SJ2
MMRRC Submission 038722-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.120) question?
Stock # R0530 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 5991555-6094565 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 6058380 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 58 (S58R)
Ref Sequence ENSEMBL: ENSMUSP00000111451 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000061091] [ENSMUST00000080283] [ENSMUST00000115784] [ENSMUST00000115785] [ENSMUST00000115786] [ENSMUST00000115787] [ENSMUST00000115791] [ENSMUST00000115790] [ENSMUST00000115788] [ENSMUST00000115789] [ENSMUST00000146009] [ENSMUST00000142409] [ENSMUST00000134767]
AlphaFold Q9D2G5
Predicted Effect possibly damaging
Transcript: ENSMUST00000061091
AA Change: S289R

PolyPhen 2 Score 0.873 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000060382
Gene: ENSMUSG00000023805
AA Change: S289R

DomainStartEndE-ValueType
Pfam:Syja_N 1 263 2.5e-72 PFAM
Blast:IPPc 394 423 3e-6 BLAST
IPPc 443 785 3.72e-128 SMART
DUF1866 778 923 1.04e-73 SMART
low complexity region 926 940 N/A INTRINSIC
low complexity region 965 976 N/A INTRINSIC
low complexity region 1012 1027 N/A INTRINSIC
low complexity region 1127 1139 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000080283
AA Change: S374R

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000079164
Gene: ENSMUSG00000023805
AA Change: S374R

DomainStartEndE-ValueType
Pfam:Syja_N 60 348 5.5e-78 PFAM
Blast:IPPc 479 508 3e-6 BLAST
IPPc 528 870 3.72e-128 SMART
DUF1866 863 1008 1.04e-73 SMART
low complexity region 1011 1025 N/A INTRINSIC
low complexity region 1050 1061 N/A INTRINSIC
low complexity region 1167 1179 N/A INTRINSIC
low complexity region 1217 1234 N/A INTRINSIC
low complexity region 1263 1277 N/A INTRINSIC
low complexity region 1293 1306 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000115784
SMART Domains Protein: ENSMUSP00000111450
Gene: ENSMUSG00000023805

DomainStartEndE-ValueType
PDB:3LWT|X 9 171 3e-12 PDB
Blast:IPPc 163 192 2e-6 BLAST
IPPc 212 554 3.72e-128 SMART
DUF1866 547 692 1.04e-73 SMART
low complexity region 695 709 N/A INTRINSIC
low complexity region 734 745 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000115785
AA Change: S58R

PolyPhen 2 Score 0.881 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000111451
Gene: ENSMUSG00000023805
AA Change: S58R

DomainStartEndE-ValueType
PDB:3LWT|X 9 171 4e-12 PDB
Blast:IPPc 163 192 2e-6 BLAST
IPPc 212 554 3.72e-128 SMART
DUF1866 547 692 1.04e-73 SMART
low complexity region 695 709 N/A INTRINSIC
low complexity region 734 745 N/A INTRINSIC
low complexity region 851 863 N/A INTRINSIC
low complexity region 901 918 N/A INTRINSIC
low complexity region 947 961 N/A INTRINSIC
low complexity region 977 990 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000115786
AA Change: S134R

PolyPhen 2 Score 0.800 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000111452
Gene: ENSMUSG00000023805
AA Change: S134R

DomainStartEndE-ValueType
Pfam:Syja_N 1 108 5.3e-29 PFAM
Blast:IPPc 239 268 1e-6 BLAST
IPPc 288 525 6e-18 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000115787
SMART Domains Protein: ENSMUSP00000111453
Gene: ENSMUSG00000023805

DomainStartEndE-ValueType
Pfam:Syja_N 1 108 5.7e-28 PFAM
Blast:IPPc 239 268 2e-6 BLAST
IPPc 288 630 3.72e-128 SMART
DUF1866 623 768 1.04e-73 SMART
low complexity region 771 785 N/A INTRINSIC
low complexity region 810 821 N/A INTRINSIC
low complexity region 927 939 N/A INTRINSIC
low complexity region 977 994 N/A INTRINSIC
low complexity region 1023 1037 N/A INTRINSIC
low complexity region 1053 1066 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115791
AA Change: S374R

PolyPhen 2 Score 0.352 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000111457
Gene: ENSMUSG00000023805
AA Change: S374R

DomainStartEndE-ValueType
Pfam:Syja_N 61 343 8.5e-67 PFAM
Blast:IPPc 479 508 3e-6 BLAST
IPPc 528 870 3.72e-128 SMART
DUF1866 863 1008 1.04e-73 SMART
low complexity region 1011 1025 N/A INTRINSIC
low complexity region 1050 1061 N/A INTRINSIC
low complexity region 1097 1112 N/A INTRINSIC
low complexity region 1212 1224 N/A INTRINSIC
low complexity region 1262 1279 N/A INTRINSIC
low complexity region 1308 1322 N/A INTRINSIC
low complexity region 1338 1351 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000115790
AA Change: S289R

PolyPhen 2 Score 0.800 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000111456
Gene: ENSMUSG00000023805
AA Change: S289R

DomainStartEndE-ValueType
Pfam:Syja_N 1 263 3e-72 PFAM
Blast:IPPc 394 423 3e-6 BLAST
IPPc 443 785 3.72e-128 SMART
DUF1866 778 923 1.04e-73 SMART
low complexity region 926 940 N/A INTRINSIC
low complexity region 965 976 N/A INTRINSIC
low complexity region 1012 1027 N/A INTRINSIC
low complexity region 1127 1139 N/A INTRINSIC
low complexity region 1177 1194 N/A INTRINSIC
low complexity region 1223 1237 N/A INTRINSIC
low complexity region 1253 1266 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000115788
SMART Domains Protein: ENSMUSP00000111454
Gene: ENSMUSG00000023805

DomainStartEndE-ValueType
Pfam:Syja_N 1 108 4.8e-28 PFAM
Blast:IPPc 239 268 2e-6 BLAST
IPPc 288 630 3.72e-128 SMART
DUF1866 623 768 1.04e-73 SMART
low complexity region 771 785 N/A INTRINSIC
low complexity region 810 821 N/A INTRINSIC
low complexity region 927 939 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000115789
SMART Domains Protein: ENSMUSP00000111455
Gene: ENSMUSG00000023805

DomainStartEndE-ValueType
Pfam:Syja_N 1 187 2.3e-60 PFAM
Blast:IPPc 318 347 2e-6 BLAST
IPPc 367 709 3.72e-128 SMART
DUF1866 702 847 1.04e-73 SMART
low complexity region 850 864 N/A INTRINSIC
low complexity region 889 900 N/A INTRINSIC
low complexity region 1006 1018 N/A INTRINSIC
low complexity region 1056 1073 N/A INTRINSIC
low complexity region 1102 1116 N/A INTRINSIC
low complexity region 1132 1145 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000146009
AA Change: S374R

PolyPhen 2 Score 0.067 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000122381
Gene: ENSMUSG00000023805
AA Change: S374R

DomainStartEndE-ValueType
Pfam:Syja_N 60 348 3.6e-78 PFAM
Blast:IPPc 479 508 3e-6 BLAST
IPPc 528 870 3.72e-128 SMART
DUF1866 863 1008 1.04e-73 SMART
low complexity region 1011 1025 N/A INTRINSIC
low complexity region 1050 1061 N/A INTRINSIC
low complexity region 1097 1112 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000142409
AA Change: S134R

PolyPhen 2 Score 0.281 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000120006
Gene: ENSMUSG00000023805
AA Change: S134R

DomainStartEndE-ValueType
Pfam:Syja_N 1 108 2.5e-28 PFAM
Blast:IPPc 239 268 2e-6 BLAST
IPPc 288 630 3.72e-128 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130661
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232567
Predicted Effect probably benign
Transcript: ENSMUST00000134767
Meta Mutation Damage Score 0.1076 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.7%
  • 10x: 96.6%
  • 20x: 93.1%
Validation Efficiency 96% (51/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
PHENOTYPE: Homozygotes for an ENU-induced allele show progressive hearing loss and cochlear hair cell degeneration associated with fusion of stereocilia followed by total loss of hair bundles and cochlear ganglion degeneration. No vestibular dysfunction or other behavioral deficits are observed. [provided by MGI curators]
Allele List at MGI

All alleles(5) : Targeted, other(1) Gene trapped(4)

Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg3 A G 5: 105,083,920 (GRCm39) W617R probably damaging Het
Adam34l A T 8: 44,079,568 (GRCm39) C219S probably benign Het
Cep83 A T 10: 94,555,450 (GRCm39) probably benign Het
Ces1e G A 8: 93,946,149 (GRCm39) probably benign Het
Ckap2 A G 8: 22,665,988 (GRCm39) probably benign Het
Clip1 C A 5: 123,778,594 (GRCm39) R443L probably damaging Het
Clmp A G 9: 40,672,302 (GRCm39) D44G probably benign Het
Cntnap2 G A 6: 46,506,839 (GRCm39) Q304* probably null Het
Cst7 A T 2: 150,412,435 (GRCm39) probably benign Het
Dclk3 A T 9: 111,311,789 (GRCm39) Y677F probably damaging Het
Dlat G T 9: 50,548,869 (GRCm39) N562K probably damaging Het
Elmod1 A T 9: 53,833,260 (GRCm39) Y182N probably damaging Het
Fzd10 T C 5: 128,679,077 (GRCm39) F266L probably damaging Het
Gm8258 A G 5: 104,923,952 (GRCm39) noncoding transcript Het
Gm9742 T A 13: 8,080,041 (GRCm39) noncoding transcript Het
Hdlbp T C 1: 93,358,039 (GRCm39) probably benign Het
Itga8 A G 2: 12,196,627 (GRCm39) S597P probably damaging Het
Kndc1 A T 7: 139,481,153 (GRCm39) I80F probably damaging Het
Ktn1 A G 14: 47,970,700 (GRCm39) N1192S probably benign Het
Ldha G A 7: 46,503,417 (GRCm39) V270M probably damaging Het
Lyst T C 13: 13,931,891 (GRCm39) probably benign Het
Map3k9 A T 12: 81,769,256 (GRCm39) F954I probably benign Het
Mroh2b A G 15: 4,963,877 (GRCm39) N823S probably damaging Het
Mycbp2 A T 14: 103,419,895 (GRCm39) N2480K probably damaging Het
Nat1 A G 8: 67,943,977 (GRCm39) K121E probably benign Het
Neurl1b T A 17: 26,660,519 (GRCm39) probably null Het
Nnt C A 13: 119,531,257 (GRCm39) L163F probably damaging Het
Or10v5 A G 19: 11,805,556 (GRCm39) V278A probably benign Het
Otog A G 7: 45,947,668 (GRCm39) T2274A probably damaging Het
Pde4b G A 4: 102,459,848 (GRCm39) R561Q probably damaging Het
Pitpnm2 A G 5: 124,269,264 (GRCm39) F453L probably damaging Het
Pms1 T C 1: 53,235,972 (GRCm39) probably null Het
Pot1a A G 6: 25,771,540 (GRCm39) V227A possibly damaging Het
Prdx6b A G 2: 80,123,659 (GRCm39) N156S probably damaging Het
Ptpn9 A G 9: 56,968,417 (GRCm39) S586G probably benign Het
Serpina6 A T 12: 103,618,053 (GRCm39) N253K probably damaging Het
Slc12a2 T A 18: 58,052,608 (GRCm39) V809D possibly damaging Het
Slc2a8 C T 2: 32,863,696 (GRCm39) A449T probably benign Het
Slc6a6 A G 6: 91,701,939 (GRCm39) I116V probably null Het
Tafa3 T C 3: 104,679,487 (GRCm39) probably benign Het
Tktl2 T C 8: 66,965,831 (GRCm39) V463A probably damaging Het
Uchl5 T C 1: 143,670,082 (GRCm39) V105A possibly damaging Het
Usp9y T C Y: 1,333,600 (GRCm39) probably benign Het
Vmn1r200 T C 13: 22,579,667 (GRCm39) S148P probably damaging Het
Vmn2r50 A T 7: 9,781,644 (GRCm39) M367K possibly damaging Het
Vps13a T C 19: 16,632,570 (GRCm39) probably benign Het
Wdr26 A T 1: 181,013,635 (GRCm39) probably null Het
Wdr87-ps A G 7: 29,229,545 (GRCm39) noncoding transcript Het
Ythdc2 T A 18: 44,983,465 (GRCm39) M544K probably damaging Het
Zpld2 A G 4: 133,930,221 (GRCm39) I28T probably benign Het
Other mutations in Synj2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01067:Synj2 APN 17 6,088,201 (GRCm39) missense possibly damaging 0.48
IGL01399:Synj2 APN 17 6,060,046 (GRCm39) missense probably damaging 1.00
IGL01793:Synj2 APN 17 6,088,321 (GRCm39) missense probably benign 0.01
IGL01793:Synj2 APN 17 6,077,500 (GRCm39) nonsense probably null
IGL02096:Synj2 APN 17 6,040,628 (GRCm39) missense probably damaging 1.00
IGL02115:Synj2 APN 17 6,067,865 (GRCm39) missense probably damaging 1.00
IGL02222:Synj2 APN 17 6,087,755 (GRCm39) missense probably benign 0.04
IGL02478:Synj2 APN 17 6,088,199 (GRCm39) missense probably benign 0.00
IGL02634:Synj2 APN 17 6,080,035 (GRCm39) missense probably damaging 1.00
IGL02652:Synj2 APN 17 6,067,868 (GRCm39) missense probably damaging 1.00
IGL02681:Synj2 APN 17 6,040,611 (GRCm39) missense probably damaging 1.00
IGL02719:Synj2 APN 17 6,047,192 (GRCm39) missense probably benign 0.02
IGL03253:Synj2 APN 17 6,053,434 (GRCm39) splice site probably null
IGL03365:Synj2 APN 17 6,069,679 (GRCm39) missense probably damaging 1.00
I2288:Synj2 UTSW 17 6,072,542 (GRCm39) splice site probably benign
I2289:Synj2 UTSW 17 6,072,542 (GRCm39) splice site probably benign
R0389:Synj2 UTSW 17 6,080,058 (GRCm39) missense probably benign 0.35
R0433:Synj2 UTSW 17 6,084,123 (GRCm39) missense probably damaging 1.00
R0539:Synj2 UTSW 17 6,047,163 (GRCm39) start codon destroyed probably null 0.63
R0556:Synj2 UTSW 17 6,088,230 (GRCm39) nonsense probably null
R1263:Synj2 UTSW 17 6,069,634 (GRCm39) missense probably damaging 0.99
R1443:Synj2 UTSW 17 6,073,940 (GRCm39) missense probably damaging 0.99
R1450:Synj2 UTSW 17 6,077,599 (GRCm39) splice site probably benign
R1532:Synj2 UTSW 17 6,084,194 (GRCm39) missense probably benign 0.00
R1542:Synj2 UTSW 17 6,075,292 (GRCm39) missense probably benign 0.01
R1809:Synj2 UTSW 17 6,076,826 (GRCm39) missense possibly damaging 0.95
R1875:Synj2 UTSW 17 6,078,825 (GRCm39) missense possibly damaging 0.69
R1897:Synj2 UTSW 17 6,072,412 (GRCm39) nonsense probably null
R1928:Synj2 UTSW 17 6,040,542 (GRCm39) missense probably damaging 0.99
R2008:Synj2 UTSW 17 6,047,221 (GRCm39) missense probably damaging 1.00
R2060:Synj2 UTSW 17 6,087,755 (GRCm39) missense probably benign 0.04
R2109:Synj2 UTSW 17 6,063,966 (GRCm39) missense probably benign 0.00
R2332:Synj2 UTSW 17 6,074,069 (GRCm39) missense probably damaging 0.99
R2413:Synj2 UTSW 17 6,078,849 (GRCm39) missense probably damaging 1.00
R3684:Synj2 UTSW 17 6,078,718 (GRCm39) missense probably damaging 0.97
R4111:Synj2 UTSW 17 6,058,240 (GRCm39) missense probably benign 0.02
R4113:Synj2 UTSW 17 6,058,240 (GRCm39) missense probably benign 0.02
R4654:Synj2 UTSW 17 6,063,813 (GRCm39) missense probably damaging 1.00
R4797:Synj2 UTSW 17 6,084,163 (GRCm39) missense probably damaging 1.00
R4812:Synj2 UTSW 17 6,060,939 (GRCm39) missense probably damaging 1.00
R4873:Synj2 UTSW 17 6,038,343 (GRCm39) intron probably benign
R4875:Synj2 UTSW 17 6,038,343 (GRCm39) intron probably benign
R5110:Synj2 UTSW 17 6,087,990 (GRCm39) missense probably benign 0.06
R5205:Synj2 UTSW 17 5,991,793 (GRCm39) missense probably damaging 1.00
R5504:Synj2 UTSW 17 6,086,750 (GRCm39) missense possibly damaging 0.85
R5593:Synj2 UTSW 17 6,088,390 (GRCm39) makesense probably null
R5690:Synj2 UTSW 17 6,085,802 (GRCm39) missense probably benign 0.00
R5870:Synj2 UTSW 17 6,088,128 (GRCm39) missense probably benign 0.00
R6084:Synj2 UTSW 17 6,088,373 (GRCm39) missense probably damaging 1.00
R6084:Synj2 UTSW 17 6,067,889 (GRCm39) missense probably damaging 0.98
R6158:Synj2 UTSW 17 6,036,487 (GRCm39) missense probably benign 0.00
R6159:Synj2 UTSW 17 6,036,327 (GRCm39) missense probably damaging 1.00
R6160:Synj2 UTSW 17 6,058,336 (GRCm39) missense possibly damaging 0.92
R6278:Synj2 UTSW 17 6,026,149 (GRCm39) missense probably damaging 1.00
R6406:Synj2 UTSW 17 6,069,846 (GRCm39) intron probably benign
R6531:Synj2 UTSW 17 6,084,114 (GRCm39) missense probably damaging 1.00
R6729:Synj2 UTSW 17 6,036,289 (GRCm39) start codon destroyed probably null 1.00
R6774:Synj2 UTSW 17 6,088,290 (GRCm39) missense possibly damaging 0.87
R6792:Synj2 UTSW 17 6,040,565 (GRCm39) missense probably benign 0.01
R6844:Synj2 UTSW 17 6,026,081 (GRCm39) missense probably damaging 0.96
R6865:Synj2 UTSW 17 6,067,844 (GRCm39) nonsense probably null
R7178:Synj2 UTSW 17 6,076,754 (GRCm39) missense possibly damaging 0.95
R7286:Synj2 UTSW 17 6,088,220 (GRCm39) missense possibly damaging 0.79
R7403:Synj2 UTSW 17 6,088,005 (GRCm39) missense possibly damaging 0.76
R7451:Synj2 UTSW 17 6,080,066 (GRCm39) missense possibly damaging 0.68
R7501:Synj2 UTSW 17 6,040,514 (GRCm39) missense possibly damaging 0.79
R7730:Synj2 UTSW 17 6,066,562 (GRCm39) missense probably benign 0.33
R7799:Synj2 UTSW 17 6,088,098 (GRCm39) missense probably benign 0.10
R7804:Synj2 UTSW 17 6,069,809 (GRCm39) missense unknown
R7841:Synj2 UTSW 17 6,094,419 (GRCm39) missense unknown
R8347:Synj2 UTSW 17 6,060,060 (GRCm39) missense probably damaging 1.00
R8358:Synj2 UTSW 17 6,074,080 (GRCm39) nonsense probably null
R8391:Synj2 UTSW 17 5,991,796 (GRCm39) missense probably damaging 0.99
R8725:Synj2 UTSW 17 6,088,015 (GRCm39) missense possibly damaging 0.48
R8787:Synj2 UTSW 17 6,036,514 (GRCm39) missense possibly damaging 0.57
R8877:Synj2 UTSW 17 6,087,941 (GRCm39) missense probably damaging 1.00
R9091:Synj2 UTSW 17 6,067,875 (GRCm39) missense possibly damaging 0.88
R9121:Synj2 UTSW 17 6,040,599 (GRCm39) missense probably damaging 1.00
R9147:Synj2 UTSW 17 6,084,172 (GRCm39) missense probably damaging 1.00
R9148:Synj2 UTSW 17 6,084,172 (GRCm39) missense probably damaging 1.00
R9270:Synj2 UTSW 17 6,067,875 (GRCm39) missense possibly damaging 0.88
R9489:Synj2 UTSW 17 6,063,794 (GRCm39) missense probably benign 0.00
R9605:Synj2 UTSW 17 6,063,794 (GRCm39) missense probably benign 0.00
R9720:Synj2 UTSW 17 6,040,584 (GRCm39) missense probably benign
R9773:Synj2 UTSW 17 6,094,232 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TGCCCATATGCAGGCAAGATGC -3'
(R):5'- AGTGAGGAGGACCCCAGATCACTAAC -3'

Sequencing Primer
(F):5'- CCACAGCTAATGTACTCTAGTGGG -3'
(R):5'- GATCACTAACATCACAGAGCTTATG -3'
Posted On 2013-06-12