Incidental Mutation 'R0390:Sema6d'
ID 31572
Institutional Source Beutler Lab
Gene Symbol Sema6d
Ensembl Gene ENSMUSG00000027200
Gene Name sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D
Synonyms Sema6D-6, 1110067B02Rik, Sema6D-1, Sema6D-4, Sema6D-5, Sema6D-2
MMRRC Submission 038596-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0390 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 123931889-124509690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 124500410 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 393 (I393N)
Ref Sequence ENSEMBL: ENSMUSP00000099531 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051419] [ENSMUST00000076335] [ENSMUST00000077847] [ENSMUST00000078621] [ENSMUST00000103238] [ENSMUST00000103239] [ENSMUST00000103240] [ENSMUST00000103241]
AlphaFold Q76KF0
Predicted Effect probably damaging
Transcript: ENSMUST00000051419
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 582 4.57e-1 SMART
transmembrane domain 602 624 N/A INTRINSIC
low complexity region 743 764 N/A INTRINSIC
internal_repeat_1 797 898 7.43e-5 PROSPERO
internal_repeat_1 892 1004 7.43e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000076335
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
transmembrane domain 589 611 N/A INTRINSIC
low complexity region 730 751 N/A INTRINSIC
internal_repeat_1 784 885 7.28e-5 PROSPERO
internal_repeat_1 879 991 7.28e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000077847
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
low complexity region 573 584 N/A INTRINSIC
transmembrane domain 645 667 N/A INTRINSIC
low complexity region 786 807 N/A INTRINSIC
internal_repeat_1 840 941 5.95e-5 PROSPERO
internal_repeat_1 935 1047 5.95e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000078621
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 582 4.57e-1 SMART
transmembrane domain 621 643 N/A INTRINSIC
low complexity region 762 783 N/A INTRINSIC
internal_repeat_1 816 917 8.83e-5 PROSPERO
internal_repeat_1 911 1023 8.83e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000103238
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
low complexity region 573 584 N/A INTRINSIC
transmembrane domain 645 667 N/A INTRINSIC
low complexity region 786 807 N/A INTRINSIC
internal_repeat_1 840 941 5.95e-5 PROSPERO
internal_repeat_1 935 1047 5.95e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000103239
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
low complexity region 587 603 N/A INTRINSIC
transmembrane domain 664 686 N/A INTRINSIC
low complexity region 805 826 N/A INTRINSIC
internal_repeat_1 859 960 5.78e-5 PROSPERO
internal_repeat_1 954 1066 5.78e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000103240
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
low complexity region 587 603 N/A INTRINSIC
transmembrane domain 660 682 N/A INTRINSIC
low complexity region 801 822 N/A INTRINSIC
internal_repeat_1 855 956 5.63e-5 PROSPERO
internal_repeat_1 950 1062 5.63e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000103241
AA Change: I393N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: I393N

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 57 487 7.29e-184 SMART
PSI 514 569 1.12e-1 SMART
transmembrane domain 589 611 N/A INTRINSIC
low complexity region 730 751 N/A INTRINSIC
internal_repeat_1 784 885 7.28e-5 PROSPERO
internal_repeat_1 879 991 7.28e-5 PROSPERO
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132088
Meta Mutation Damage Score 0.9305 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.1%
  • 10x: 95.9%
  • 20x: 92.0%
Validation Efficiency 98% (110/112)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal dendritic cell trafficking and antigen-specific T cell priming. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 110 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 C T 8: 25,164,070 (GRCm39) G38R probably benign Het
Ap2m1 T C 16: 20,359,849 (GRCm39) M183T probably damaging Het
Apob A T 12: 8,038,678 (GRCm39) I364F probably damaging Het
Arl6 A T 16: 59,442,784 (GRCm39) probably benign Het
Cand2 A G 6: 115,751,614 (GRCm39) M15V possibly damaging Het
Cbl A G 9: 44,112,302 (GRCm39) F131S probably damaging Het
Ccdc74a A G 16: 17,468,340 (GRCm39) S321G probably benign Het
Cdc14b T C 13: 64,358,006 (GRCm39) probably benign Het
Cep152 T C 2: 125,418,789 (GRCm39) probably benign Het
Cep290 A G 10: 100,344,620 (GRCm39) E479G probably benign Het
Chrm2 T G 6: 36,501,046 (GRCm39) I301R probably benign Het
Clec2e A G 6: 129,070,431 (GRCm39) W197R probably damaging Het
Cnot10 G T 9: 114,458,218 (GRCm39) S96* probably null Het
Col19a1 A G 1: 24,328,736 (GRCm39) probably benign Het
Csmd2 T C 4: 128,027,466 (GRCm39) probably benign Het
Cthrc1 A T 15: 38,950,159 (GRCm39) *172L probably null Het
Cul9 A T 17: 46,839,515 (GRCm39) I821N probably benign Het
Daam1 G C 12: 72,022,078 (GRCm39) probably benign Het
Dhx58 A T 11: 100,590,090 (GRCm39) I398N probably damaging Het
Dip2b T A 15: 100,091,794 (GRCm39) H844Q probably damaging Het
Dmac2 A G 7: 25,320,454 (GRCm39) D50G probably damaging Het
Dmxl1 C A 18: 50,012,429 (GRCm39) Q1529K probably benign Het
Dtna C T 18: 23,730,558 (GRCm39) P315L probably damaging Het
Ep300 T C 15: 81,524,317 (GRCm39) S1382P unknown Het
Fat2 A T 11: 55,201,603 (GRCm39) N490K probably damaging Het
Flg2 T A 3: 93,107,662 (GRCm39) probably benign Het
Gpatch1 T C 7: 34,980,806 (GRCm39) probably benign Het
Grin2a C A 16: 9,397,449 (GRCm39) K879N possibly damaging Het
Hacd3 A C 9: 64,908,304 (GRCm39) I164S possibly damaging Het
Hinfp A C 9: 44,210,245 (GRCm39) C197G probably damaging Het
Hsd17b12 T C 2: 93,945,335 (GRCm39) probably benign Het
Hsd3b1 A T 3: 98,760,355 (GRCm39) L212Q probably damaging Het
Ifrd1 C T 12: 40,264,093 (GRCm39) probably null Het
Igf2bp2 A G 16: 21,900,551 (GRCm39) F129L possibly damaging Het
Kirrel3 T A 9: 34,931,459 (GRCm39) I409N probably damaging Het
Klhdc10 T C 6: 30,447,411 (GRCm39) I204T probably damaging Het
Kpna6 A T 4: 129,551,597 (GRCm39) S65R possibly damaging Het
Lama3 A T 18: 12,540,620 (GRCm39) D308V probably benign Het
Larp4b T A 13: 9,208,143 (GRCm39) probably null Het
Lgr6 C T 1: 134,921,748 (GRCm39) A199T probably damaging Het
Lyzl1 A T 18: 4,169,175 (GRCm39) T11S probably benign Het
Man1c1 A G 4: 134,305,626 (GRCm39) L366P probably damaging Het
Mef2a A G 7: 66,901,472 (GRCm39) M100T probably damaging Het
Mettl13 G A 1: 162,366,458 (GRCm39) H474Y possibly damaging Het
Minar2 T A 18: 59,208,760 (GRCm39) V136E probably damaging Het
Mmp3 A G 9: 7,451,320 (GRCm39) D352G probably benign Het
Mns1 T C 9: 72,360,086 (GRCm39) I412T probably damaging Het
Mon2 T C 10: 122,842,926 (GRCm39) D1501G probably null Het
Mylk G T 16: 34,695,990 (GRCm39) G242W probably damaging Het
Nav1 T C 1: 135,377,704 (GRCm39) D1715G possibly damaging Het
Nckap1l T C 15: 103,362,310 (GRCm39) S2P probably damaging Het
Nek3 A T 8: 22,618,745 (GRCm39) probably benign Het
Nfrkb A G 9: 31,300,193 (GRCm39) probably benign Het
Nlrp4d T C 7: 10,122,705 (GRCm39) D53G probably benign Het
Nol8 T C 13: 49,815,628 (GRCm39) S561P probably damaging Het
Nuf2 A C 1: 169,352,866 (GRCm39) probably benign Het
Odad3 T A 9: 21,903,004 (GRCm39) H442L probably benign Het
Ofcc1 T A 13: 40,168,789 (GRCm39) D866V possibly damaging Het
Optn A G 2: 5,051,006 (GRCm39) L125P probably benign Het
Or5k3 A G 16: 58,969,662 (GRCm39) I150V probably benign Het
Otoa T A 7: 120,730,564 (GRCm39) F588Y probably benign Het
Pappa T A 4: 65,269,850 (GRCm39) probably null Het
Pde5a T G 3: 122,629,232 (GRCm39) C635W probably damaging Het
Pdgfb A T 15: 79,887,620 (GRCm39) probably null Het
Pih1d2 T A 9: 50,532,346 (GRCm39) C135S probably damaging Het
Plcg1 G T 2: 160,594,286 (GRCm39) C361F probably damaging Het
Ppp4r4 T C 12: 103,567,619 (GRCm39) probably benign Het
Pramel26 T A 4: 143,538,269 (GRCm39) D234V probably benign Het
Prdm10 G A 9: 31,260,564 (GRCm39) probably null Het
Prex2 T A 1: 11,159,930 (GRCm39) probably null Het
Prss56 T G 1: 87,112,452 (GRCm39) probably null Het
Prtg A G 9: 72,752,240 (GRCm39) K209E probably benign Het
Ptprc G A 1: 138,050,313 (GRCm39) T36I possibly damaging Het
Rasgrp4 A G 7: 28,845,285 (GRCm39) Y302C probably damaging Het
Rb1cc1 T A 1: 6,318,858 (GRCm39) M759K probably damaging Het
Rbm15b T A 9: 106,763,197 (GRCm39) M324L probably benign Het
Rcbtb2 T C 14: 73,415,987 (GRCm39) V500A probably damaging Het
Rgs6 A G 12: 83,180,451 (GRCm39) K434R probably damaging Het
Rims1 C T 1: 22,635,607 (GRCm39) A125T possibly damaging Het
Robo3 A G 9: 37,333,473 (GRCm39) V746A probably benign Het
Rtl1 C T 12: 109,557,820 (GRCm39) E1340K unknown Het
Sacs G A 14: 61,443,089 (GRCm39) D1712N possibly damaging Het
Samd4b G A 7: 28,103,402 (GRCm39) P19S probably benign Het
Samhd1 T C 2: 156,956,151 (GRCm39) Y347C probably damaging Het
Sigmar1 C T 4: 41,741,243 (GRCm39) A4T probably benign Het
Skint9 C A 4: 112,246,376 (GRCm39) L245F probably benign Het
Slc35f5 T C 1: 125,512,832 (GRCm39) L372P probably damaging Het
Smc1b A T 15: 84,950,478 (GRCm39) I1182N probably damaging Het
Smyd3 A G 1: 178,785,138 (GRCm39) probably benign Het
Sptlc1 T C 13: 53,491,648 (GRCm39) D417G probably benign Het
Sv2c T C 13: 96,225,216 (GRCm39) N31S probably benign Het
Tjp1 T C 7: 64,964,738 (GRCm39) D811G probably damaging Het
Top2b A G 14: 16,418,442 (GRCm38) T1221A probably benign Het
Tph2 T C 10: 115,010,014 (GRCm39) D182G probably damaging Het
Traf6 C T 2: 101,518,933 (GRCm39) Q141* probably null Het
Ttn T C 2: 76,587,275 (GRCm39) D21574G probably damaging Het
Uba2 T A 7: 33,850,446 (GRCm39) N367I probably benign Het
Ube2b T C 11: 51,879,429 (GRCm39) probably benign Het
Ubr5 G T 15: 38,030,916 (GRCm39) L426I probably benign Het
Ugt2a2 T A 5: 87,612,007 (GRCm39) H301L probably benign Het
Upf2 T A 2: 6,023,705 (GRCm39) probably benign Het
Utrn T C 10: 12,585,804 (GRCm39) D991G probably benign Het
Vmn2r25 T C 6: 123,800,140 (GRCm39) D734G probably damaging Het
Vmn2r68 C G 7: 84,882,466 (GRCm39) probably null Het
Vmn2r68 T A 7: 84,882,457 (GRCm39) probably benign Het
Vwf T A 6: 125,603,324 (GRCm39) Y891* probably null Het
Wwox C T 8: 115,433,018 (GRCm39) T228I probably benign Het
Zer1 C T 2: 29,998,225 (GRCm39) probably benign Het
Zfp180 C T 7: 23,804,132 (GRCm39) H184Y possibly damaging Het
Zfp68 A T 5: 138,605,487 (GRCm39) Y279N probably benign Het
Other mutations in Sema6d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00155:Sema6d APN 2 124,501,785 (GRCm39) missense possibly damaging 0.91
IGL00508:Sema6d APN 2 124,498,844 (GRCm39) splice site probably benign
IGL00710:Sema6d APN 2 124,504,208 (GRCm39) missense probably benign 0.00
IGL00811:Sema6d APN 2 124,500,389 (GRCm39) missense probably damaging 1.00
IGL01457:Sema6d APN 2 124,495,562 (GRCm39) missense unknown
IGL01524:Sema6d APN 2 124,505,995 (GRCm39) missense possibly damaging 0.86
IGL01598:Sema6d APN 2 124,507,018 (GRCm39) missense probably damaging 1.00
IGL01915:Sema6d APN 2 124,500,491 (GRCm39) splice site probably benign
IGL02365:Sema6d APN 2 124,498,788 (GRCm39) missense probably benign 0.14
IGL02698:Sema6d APN 2 124,495,643 (GRCm39) missense possibly damaging 0.95
IGL02865:Sema6d APN 2 124,505,993 (GRCm39) missense probably damaging 1.00
IGL03018:Sema6d APN 2 124,501,520 (GRCm39) missense possibly damaging 0.95
IGL03333:Sema6d APN 2 124,506,290 (GRCm39) missense possibly damaging 0.83
R0269:Sema6d UTSW 2 124,502,665 (GRCm39) missense possibly damaging 0.63
R0541:Sema6d UTSW 2 124,507,197 (GRCm39) missense probably benign 0.25
R0615:Sema6d UTSW 2 124,496,055 (GRCm39) splice site probably benign
R0617:Sema6d UTSW 2 124,502,665 (GRCm39) missense possibly damaging 0.63
R0694:Sema6d UTSW 2 124,505,961 (GRCm39) missense probably damaging 1.00
R0854:Sema6d UTSW 2 124,507,222 (GRCm39) missense probably damaging 0.97
R1630:Sema6d UTSW 2 124,506,265 (GRCm39) missense possibly damaging 0.89
R1682:Sema6d UTSW 2 124,507,069 (GRCm39) missense probably benign 0.21
R1823:Sema6d UTSW 2 124,501,476 (GRCm39) splice site probably null
R1932:Sema6d UTSW 2 124,501,806 (GRCm39) critical splice donor site probably null
R2249:Sema6d UTSW 2 124,501,508 (GRCm39) missense possibly damaging 0.54
R2256:Sema6d UTSW 2 124,506,070 (GRCm39) missense probably damaging 1.00
R2331:Sema6d UTSW 2 124,499,983 (GRCm39) missense probably damaging 1.00
R2910:Sema6d UTSW 2 124,506,957 (GRCm39) missense probably damaging 1.00
R3683:Sema6d UTSW 2 124,496,146 (GRCm39) missense possibly damaging 0.88
R3937:Sema6d UTSW 2 124,498,770 (GRCm39) missense probably benign 0.00
R4135:Sema6d UTSW 2 124,506,040 (GRCm39) missense probably damaging 0.96
R4446:Sema6d UTSW 2 124,505,979 (GRCm39) missense probably damaging 0.98
R4583:Sema6d UTSW 2 124,506,082 (GRCm39) missense probably damaging 1.00
R4599:Sema6d UTSW 2 124,496,151 (GRCm39) missense probably damaging 1.00
R4822:Sema6d UTSW 2 124,504,214 (GRCm39) missense possibly damaging 0.79
R4884:Sema6d UTSW 2 124,498,738 (GRCm39) splice site probably null
R5288:Sema6d UTSW 2 124,506,166 (GRCm39) missense probably damaging 1.00
R5443:Sema6d UTSW 2 124,498,756 (GRCm39) missense probably damaging 1.00
R5504:Sema6d UTSW 2 124,499,941 (GRCm39) missense probably damaging 1.00
R5534:Sema6d UTSW 2 124,501,735 (GRCm39) missense possibly damaging 0.75
R5615:Sema6d UTSW 2 124,498,821 (GRCm39) missense probably damaging 0.97
R5747:Sema6d UTSW 2 124,506,867 (GRCm39) missense probably damaging 0.99
R5866:Sema6d UTSW 2 124,506,262 (GRCm39) missense probably benign 0.26
R5980:Sema6d UTSW 2 124,506,628 (GRCm39) missense probably damaging 1.00
R6670:Sema6d UTSW 2 124,496,762 (GRCm39) small deletion probably benign
R6803:Sema6d UTSW 2 124,505,970 (GRCm39) missense probably damaging 0.96
R7023:Sema6d UTSW 2 124,506,831 (GRCm39) missense probably damaging 1.00
R7068:Sema6d UTSW 2 124,499,741 (GRCm39) missense probably benign
R7426:Sema6d UTSW 2 124,496,078 (GRCm39) missense probably damaging 1.00
R7556:Sema6d UTSW 2 124,496,109 (GRCm39) missense probably damaging 1.00
R7569:Sema6d UTSW 2 124,499,892 (GRCm39) missense possibly damaging 0.92
R8427:Sema6d UTSW 2 124,507,197 (GRCm39) missense probably benign 0.25
R8690:Sema6d UTSW 2 124,506,937 (GRCm39) missense probably benign 0.07
R8711:Sema6d UTSW 2 124,502,232 (GRCm39) missense possibly damaging 0.54
R8757:Sema6d UTSW 2 124,497,134 (GRCm39) missense probably damaging 1.00
R8759:Sema6d UTSW 2 124,497,134 (GRCm39) missense probably damaging 1.00
R8868:Sema6d UTSW 2 124,496,114 (GRCm39) missense probably damaging 1.00
R9511:Sema6d UTSW 2 124,499,943 (GRCm39) missense probably damaging 1.00
R9586:Sema6d UTSW 2 124,496,096 (GRCm39) missense probably damaging 1.00
R9731:Sema6d UTSW 2 124,506,117 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCCTCCGAGGCCAATACATGTTATC -3'
(R):5'- TGCTGAACGGTCCACTTCGATG -3'

Sequencing Primer
(F):5'- CTGGGAAATGACATTACTGCTC -3'
(R):5'- GGCTGTCAACCTGTACCTAGTG -3'
Posted On 2013-04-24