Incidental Mutation 'R0471:Syne3'
ID 46781
Institutional Source Beutler Lab
Gene Symbol Syne3
Ensembl Gene ENSMUSG00000054150
Gene Name spectrin repeat containing, nuclear envelope family member 3
Synonyms 4831426I19Rik, nesprin-3beta, nesprin-3alpha, nesprin-3
MMRRC Submission 038671-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0471 (G1)
Quality Score 153
Status Validated
Chromosome 12
Chromosomal Location 104896192-104976068 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 104909685 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 717 (H717R)
Ref Sequence ENSEMBL: ENSMUSP00000105553 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000067005] [ENSMUST00000095439] [ENSMUST00000109927]
AlphaFold Q4FZC9
Predicted Effect probably benign
Transcript: ENSMUST00000067005
AA Change: H717R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000065771
Gene: ENSMUSG00000054150
AA Change: H717R

DomainStartEndE-ValueType
Blast:SPEC 29 127 8e-24 BLAST
SPEC 136 237 1.01e-1 SMART
Blast:SPEC 252 446 9e-55 BLAST
low complexity region 447 459 N/A INTRINSIC
low complexity region 495 514 N/A INTRINSIC
SPEC 563 664 1.74e-1 SMART
Blast:SPEC 722 818 1e-12 BLAST
KASH 832 888 7.52e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000095439
AA Change: H804R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000093090
Gene: ENSMUSG00000054150
AA Change: H804R

DomainStartEndE-ValueType
SPEC 7 109 1.22e-1 SMART
SPEC 223 324 1.01e-1 SMART
Blast:SPEC 339 533 2e-54 BLAST
low complexity region 534 546 N/A INTRINSIC
low complexity region 582 601 N/A INTRINSIC
SPEC 650 751 1.74e-1 SMART
Blast:SPEC 809 905 1e-12 BLAST
KASH 919 975 7.52e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000109927
AA Change: H717R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000105553
Gene: ENSMUSG00000054150
AA Change: H717R

DomainStartEndE-ValueType
Blast:SPEC 29 127 8e-24 BLAST
SPEC 136 237 1.01e-1 SMART
Blast:SPEC 252 446 9e-55 BLAST
low complexity region 447 459 N/A INTRINSIC
low complexity region 495 514 N/A INTRINSIC
SPEC 563 664 1.74e-1 SMART
Blast:SPEC 722 818 1e-12 BLAST
KASH 832 888 7.52e-24 SMART
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 100% (67/67)
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acp6 T C 3: 97,075,891 (GRCm39) probably null Het
Adam33 C A 2: 130,896,399 (GRCm39) G437C probably damaging Het
Aldh1a1 T A 19: 20,579,377 (GRCm39) M1K probably null Het
Amotl2 C A 9: 102,597,718 (GRCm39) P126Q probably damaging Het
Ap1g1 T A 8: 110,580,275 (GRCm39) M576K possibly damaging Het
Apob C A 12: 8,040,406 (GRCm39) A581E probably damaging Het
Asb7 A T 7: 66,328,907 (GRCm39) D44E probably damaging Het
Bcl2 G A 1: 106,640,292 (GRCm39) R107C probably damaging Het
C9orf72 G A 4: 35,193,257 (GRCm39) T232I probably benign Het
Ccdc65 A T 15: 98,615,348 (GRCm39) H118L probably benign Het
Cdc25b A G 2: 131,039,204 (GRCm39) E523G probably damaging Het
Cdk11b A G 4: 155,731,999 (GRCm39) probably benign Het
Cilk1 G T 9: 78,062,799 (GRCm39) probably null Het
Clec1b A G 6: 129,378,570 (GRCm39) probably benign Het
Cntrl A G 2: 35,017,392 (GRCm39) T400A probably benign Het
Cpne4 T G 9: 104,899,481 (GRCm39) probably null Het
Cyp2j6 T A 4: 96,419,985 (GRCm39) R249* probably null Het
Dock2 T C 11: 34,579,380 (GRCm39) I678V probably benign Het
Dqx1 C T 6: 83,036,407 (GRCm39) probably benign Het
Dsp A T 13: 38,377,326 (GRCm39) K1704* probably null Het
Eif2b2 T C 12: 85,266,957 (GRCm39) F121S probably benign Het
Ephx4 T C 5: 107,561,379 (GRCm39) V69A possibly damaging Het
Epn2 T C 11: 61,426,134 (GRCm39) Q281R probably damaging Het
Fgf3 A C 7: 144,396,547 (GRCm39) D187A probably damaging Het
Galnt18 C A 7: 111,378,506 (GRCm39) probably benign Het
Gm4871 C T 5: 144,968,402 (GRCm39) probably benign Het
Inpp4b T C 8: 82,768,528 (GRCm39) I679T possibly damaging Het
Itpkb A G 1: 180,245,820 (GRCm39) E779G probably damaging Het
Itsn1 G A 16: 91,696,477 (GRCm39) V27M probably damaging Het
Lrp2 C A 2: 69,355,578 (GRCm39) R422L probably damaging Het
Mmp25 G A 17: 23,858,858 (GRCm39) A231V possibly damaging Het
Mprip T C 11: 59,650,561 (GRCm39) S1422P probably damaging Het
Mro A T 18: 74,009,860 (GRCm39) Q176L probably benign Het
Mrpl12 A G 11: 120,379,229 (GRCm39) E192G probably damaging Het
Myo5b A T 18: 74,862,025 (GRCm39) probably benign Het
Ncam2 G T 16: 80,997,772 (GRCm39) probably benign Het
Nip7 T C 8: 107,783,949 (GRCm39) L63P probably damaging Het
Nsd3 T C 8: 26,138,450 (GRCm39) probably benign Het
Nup98 A T 7: 101,788,004 (GRCm39) V1022D probably benign Het
Or2y1e T A 11: 49,218,744 (GRCm39) C169S probably damaging Het
Or5d43 A G 2: 88,104,559 (GRCm39) V278A possibly damaging Het
Or5h22 A G 16: 58,894,633 (GRCm39) I270T probably benign Het
Or7g28 A T 9: 19,272,177 (GRCm39) L158* probably null Het
P4ha2 T C 11: 54,008,434 (GRCm39) Y214H possibly damaging Het
Pacrg A T 17: 10,795,407 (GRCm39) F184L possibly damaging Het
Parpbp T A 10: 87,929,569 (GRCm39) R426S probably damaging Het
Pcdhb5 T A 18: 37,454,359 (GRCm39) Y246* probably null Het
Pik3cg T A 12: 32,244,770 (GRCm39) T895S probably damaging Het
Prkch T C 12: 73,738,426 (GRCm39) Y178H probably benign Het
Rusc2 G T 4: 43,425,486 (GRCm39) R1197L probably damaging Het
Svep1 T C 4: 58,054,700 (GRCm39) E3296G possibly damaging Het
Svs3a A G 2: 164,131,801 (GRCm39) K123R probably benign Het
Sycp2l A G 13: 41,304,006 (GRCm39) probably null Het
Tiprl A G 1: 165,050,092 (GRCm39) probably null Het
Trim24 T G 6: 37,892,130 (GRCm39) V151G possibly damaging Het
Trim33 T C 3: 103,234,217 (GRCm39) V56A possibly damaging Het
Trim67 C A 8: 125,521,397 (GRCm39) T253K probably benign Het
Trip12 T C 1: 84,703,928 (GRCm39) E698G probably damaging Het
Tspan14 T C 14: 40,637,353 (GRCm39) D145G probably damaging Het
Ushbp1 G A 8: 71,847,021 (GRCm39) Q204* probably null Het
Vmn1r71 G C 7: 10,482,019 (GRCm39) S223C possibly damaging Het
Vmn2r75 G T 7: 85,814,721 (GRCm39) N257K probably benign Het
Washc4 T C 10: 83,394,598 (GRCm39) probably benign Het
Zc3h7b G A 15: 81,666,169 (GRCm39) D560N probably damaging Het
Zscan21 T C 5: 138,123,402 (GRCm39) V27A probably benign Het
Zzef1 A C 11: 72,813,937 (GRCm39) E2842A probably damaging Het
Other mutations in Syne3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01154:Syne3 APN 12 104,924,328 (GRCm39) missense probably benign 0.00
IGL01986:Syne3 APN 12 104,934,259 (GRCm39) missense probably damaging 1.00
IGL02303:Syne3 APN 12 104,929,553 (GRCm39) missense probably damaging 1.00
IGL02469:Syne3 APN 12 104,920,565 (GRCm39) missense probably benign 0.08
IGL03127:Syne3 APN 12 104,909,687 (GRCm39) missense probably benign 0.02
BB008:Syne3 UTSW 12 104,929,491 (GRCm39) missense probably damaging 0.97
BB018:Syne3 UTSW 12 104,929,491 (GRCm39) missense probably damaging 0.97
PIT4791001:Syne3 UTSW 12 104,929,438 (GRCm39) missense probably benign
R0436:Syne3 UTSW 12 104,913,183 (GRCm39) missense possibly damaging 0.95
R0613:Syne3 UTSW 12 104,924,371 (GRCm39) missense probably benign
R0662:Syne3 UTSW 12 104,927,769 (GRCm39) missense probably benign 0.44
R0707:Syne3 UTSW 12 104,935,619 (GRCm39) missense probably damaging 0.98
R1321:Syne3 UTSW 12 104,942,055 (GRCm39) missense probably benign 0.14
R1494:Syne3 UTSW 12 104,921,841 (GRCm39) missense possibly damaging 0.87
R2035:Syne3 UTSW 12 104,924,386 (GRCm39) missense probably benign 0.00
R2147:Syne3 UTSW 12 104,919,357 (GRCm39) missense probably damaging 1.00
R2326:Syne3 UTSW 12 104,935,493 (GRCm39) missense probably damaging 1.00
R2923:Syne3 UTSW 12 104,934,343 (GRCm39) missense probably damaging 1.00
R3710:Syne3 UTSW 12 104,909,697 (GRCm39) missense possibly damaging 0.86
R3946:Syne3 UTSW 12 104,924,325 (GRCm39) missense probably damaging 1.00
R4542:Syne3 UTSW 12 104,935,503 (GRCm39) missense probably benign 0.00
R4544:Syne3 UTSW 12 104,925,728 (GRCm39) missense probably damaging 1.00
R5110:Syne3 UTSW 12 104,909,629 (GRCm39) missense probably benign 0.10
R5256:Syne3 UTSW 12 104,942,139 (GRCm39) start codon destroyed probably null 1.00
R5490:Syne3 UTSW 12 104,921,931 (GRCm39) missense probably damaging 1.00
R5616:Syne3 UTSW 12 104,921,937 (GRCm39) missense probably damaging 1.00
R5730:Syne3 UTSW 12 104,927,713 (GRCm39) missense probably benign 0.02
R5941:Syne3 UTSW 12 104,913,251 (GRCm39) missense probably benign
R6208:Syne3 UTSW 12 104,909,622 (GRCm39) missense probably benign 0.12
R6456:Syne3 UTSW 12 104,906,963 (GRCm39) missense possibly damaging 0.87
R6566:Syne3 UTSW 12 104,912,966 (GRCm39) missense probably benign 0.00
R6957:Syne3 UTSW 12 104,920,561 (GRCm39) missense probably damaging 1.00
R7251:Syne3 UTSW 12 104,927,830 (GRCm39) frame shift probably null
R7388:Syne3 UTSW 12 104,934,167 (GRCm39) missense probably damaging 1.00
R7591:Syne3 UTSW 12 104,906,863 (GRCm39) critical splice donor site probably null
R7614:Syne3 UTSW 12 104,912,901 (GRCm39) missense not run
R7740:Syne3 UTSW 12 104,920,546 (GRCm39) missense probably benign 0.01
R7763:Syne3 UTSW 12 104,963,754 (GRCm39) start gained probably benign
R7931:Syne3 UTSW 12 104,929,491 (GRCm39) missense probably damaging 0.97
R8973:Syne3 UTSW 12 104,925,654 (GRCm39) critical splice donor site probably null
R9031:Syne3 UTSW 12 104,905,871 (GRCm39) missense probably benign 0.45
R9263:Syne3 UTSW 12 104,934,415 (GRCm39) missense probably damaging 1.00
R9579:Syne3 UTSW 12 104,942,107 (GRCm39) missense probably damaging 0.96
R9665:Syne3 UTSW 12 104,924,247 (GRCm39) missense probably benign 0.01
R9668:Syne3 UTSW 12 104,898,468 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCCTTGACCAAATGGCACGAAC -3'
(R):5'- TCAGGACCCTGTAGAACTGGAACC -3'

Sequencing Primer
(F):5'- CACCATTAAGGTTACTCCTTGAGAC -3'
(R):5'- GGTACTCGACCCCTAAATGTG -3'
Posted On 2013-06-11