Incidental Mutation 'R0541:Sema6d'
ID49893
Institutional Source Beutler Lab
Gene Symbol Sema6d
Ensembl Gene ENSMUSG00000027200
Gene Namesema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D
SynonymsSema6D-6, 1110067B02Rik, Sema6D-1, Sema6D-2, Sema6D-4, Sema6D-5
MMRRC Submission 038733-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #R0541 (G1)
Quality Score225
Status Validated
Chromosome2
Chromosomal Location124089969-124667770 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 124665277 bp
ZygosityHeterozygous
Amino Acid Change Serine to Threonine at position 1045 (S1045T)
Ref Sequence ENSEMBL: ENSMUSP00000099528 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051419] [ENSMUST00000076335] [ENSMUST00000077847] [ENSMUST00000078621] [ENSMUST00000103238] [ENSMUST00000103239] [ENSMUST00000103240] [ENSMUST00000103241]
Predicted Effect probably benign
Transcript: ENSMUST00000051419
AA Change: S1002T

PolyPhen 2 Score 0.138 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: S1002T

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 possibly damaging
Transcript: ENSMUST00000076335
AA Change: S989T

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: S989T

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: S1045T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: S1045T

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 benign
Transcript: ENSMUST00000078621
AA Change: S1021T

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: S1021T

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: S1045T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: S1045T

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 benign
Transcript: ENSMUST00000103239
AA Change: S1064T

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: S1064T

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 benign
Transcript: ENSMUST00000103240
AA Change: S1060T

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: S1060T

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 possibly damaging
Transcript: ENSMUST00000103241
AA Change: S989T

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: S989T

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 0.0669 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.9%
Validation Efficiency 96% (64/67)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik T C 7: 131,139,143 M115V probably benign Het
4933415A04Rik TTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT TTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 11: 43,587,400 probably null Het
Abca7 C T 10: 80,007,351 A1220V probably benign Het
Adamts19 G A 18: 58,927,300 probably null Het
Agbl1 G A 7: 76,409,245 V194M probably benign Het
Arhgap20 G T 9: 51,849,663 S902I probably damaging Het
Atp11b T G 3: 35,806,944 D193E probably damaging Het
B3gntl1 A T 11: 121,644,604 probably benign Het
C2cd2 T C 16: 97,922,296 E7G possibly damaging Het
Camta2 A G 11: 70,681,621 L259P probably benign Het
Ccni T C 5: 93,187,704 N192D probably benign Het
Cgnl1 A G 9: 71,651,253 I946T possibly damaging Het
Chil3 T C 3: 106,161,232 probably null Het
Cntn5 A G 9: 9,673,402 probably benign Het
Cpn2 C T 16: 30,259,351 G511S possibly damaging Het
Dagla C A 19: 10,254,806 probably null Het
Dcc T C 18: 71,259,015 N1440S probably damaging Het
Drosha T A 15: 12,907,388 N1069K probably benign Het
Edc4 A G 8: 105,889,428 T812A probably benign Het
Eml4 A G 17: 83,440,042 I238V probably benign Het
Ep400 T C 5: 110,705,016 T1288A unknown Het
Fastkd1 A C 2: 69,702,406 L539R probably damaging Het
Fbln7 G A 2: 128,877,534 probably benign Het
Fbxo39 A G 11: 72,318,471 I386V probably benign Het
Gm17430 T C 18: 9,726,267 K135R probably damaging Het
Gm3646 T A 1: 39,804,323 T8S unknown Het
Gtsf1 A T 15: 103,421,192 V100E possibly damaging Het
Helz2 A G 2: 181,234,825 F1292S possibly damaging Het
Igf2bp3 G A 6: 49,107,467 probably benign Het
Ip6k2 T G 9: 108,804,627 D252E probably damaging Het
Iqck T A 7: 118,915,594 L232Q probably damaging Het
Kif18b A G 11: 102,915,175 V186A probably damaging Het
Klhl6 T A 16: 19,949,447 probably null Het
Lao1 C T 4: 118,963,802 T75I probably benign Het
Lyst T C 13: 13,681,293 F2400L probably benign Het
Map3k9 A T 12: 81,734,223 S388T possibly damaging Het
Mmp11 G T 10: 75,926,933 H229N probably damaging Het
Myh7 T G 14: 54,974,701 I1529L probably benign Het
Nckap5 G T 1: 126,695,722 D11E possibly damaging Het
Ncoa1 A T 12: 4,323,033 F123I probably damaging Het
Nelfb A T 2: 25,203,980 D385E probably benign Het
Obscn C T 11: 59,081,984 V2288M probably damaging Het
Olfr1428 C T 19: 12,109,520 V9M possibly damaging Het
Olfr1445 A G 19: 12,884,094 Y71C probably damaging Het
Olfr38 A G 6: 42,762,220 H56R probably damaging Het
Olfr686 A T 7: 105,204,160 M61K probably damaging Het
Otog T A 7: 46,269,249 probably benign Het
Oxa1l A G 14: 54,368,189 E375G possibly damaging Het
Pan2 T A 10: 128,308,222 I129K possibly damaging Het
Parp1 A G 1: 180,599,051 I919M probably benign Het
Pnpla7 T C 2: 24,995,293 Y174H probably damaging Het
Polr3b T C 10: 84,638,064 F169S probably damaging Het
Rab10 T C 12: 3,264,743 D45G probably damaging Het
Reln A G 5: 21,980,109 S1537P possibly damaging Het
Setd2 T C 9: 110,573,673 V1794A probably damaging Het
Spidr T A 16: 15,915,365 I589F probably damaging Het
Stmn4 A C 14: 66,357,939 I165L probably benign Het
Stx5a T C 19: 8,749,937 M177T probably damaging Het
Tll1 T C 8: 64,038,452 probably null Het
Tmem192 T C 8: 64,964,260 Y168H probably damaging Het
Ttc21a C T 9: 119,956,826 probably benign Het
Ush2a A G 1: 188,714,466 probably benign Het
Vezf1 A G 11: 88,081,577 M255V possibly damaging Het
Vmn2r25 A G 6: 123,839,827 F265S probably damaging Het
Vps13a A G 19: 16,704,577 S1021P probably benign Het
Wfdc16 T C 2: 164,635,853 E92G possibly damaging Het
Zkscan2 T C 7: 123,480,200 T845A possibly damaging Het
Other mutations in Sema6d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00155:Sema6d APN 2 124659865 missense possibly damaging 0.91
IGL00508:Sema6d APN 2 124656924 splice site probably benign
IGL00710:Sema6d APN 2 124662288 missense probably benign 0.00
IGL00811:Sema6d APN 2 124658469 missense probably damaging 1.00
IGL01457:Sema6d APN 2 124653642 missense unknown
IGL01524:Sema6d APN 2 124664075 missense possibly damaging 0.86
IGL01598:Sema6d APN 2 124665098 missense probably damaging 1.00
IGL01915:Sema6d APN 2 124658571 splice site probably benign
IGL02365:Sema6d APN 2 124656868 missense probably benign 0.14
IGL02698:Sema6d APN 2 124653723 missense possibly damaging 0.95
IGL02865:Sema6d APN 2 124664073 missense probably damaging 1.00
IGL03018:Sema6d APN 2 124659600 missense possibly damaging 0.95
IGL03333:Sema6d APN 2 124664370 missense possibly damaging 0.83
R0269:Sema6d UTSW 2 124660745 missense possibly damaging 0.63
R0390:Sema6d UTSW 2 124658490 missense probably damaging 1.00
R0615:Sema6d UTSW 2 124654135 splice site probably benign
R0617:Sema6d UTSW 2 124660745 missense possibly damaging 0.63
R0694:Sema6d UTSW 2 124664041 missense probably damaging 1.00
R0854:Sema6d UTSW 2 124665302 missense probably damaging 0.97
R1630:Sema6d UTSW 2 124664345 missense possibly damaging 0.89
R1682:Sema6d UTSW 2 124665149 missense probably benign 0.21
R1823:Sema6d UTSW 2 124659556 splice site probably null
R1932:Sema6d UTSW 2 124659886 critical splice donor site probably null
R2249:Sema6d UTSW 2 124659588 missense possibly damaging 0.54
R2256:Sema6d UTSW 2 124664150 missense probably damaging 1.00
R2331:Sema6d UTSW 2 124658063 missense probably damaging 1.00
R2910:Sema6d UTSW 2 124665037 missense probably damaging 1.00
R3683:Sema6d UTSW 2 124654226 missense possibly damaging 0.88
R3937:Sema6d UTSW 2 124656850 missense probably benign 0.00
R4135:Sema6d UTSW 2 124664120 missense probably damaging 0.96
R4446:Sema6d UTSW 2 124664059 missense probably damaging 0.98
R4583:Sema6d UTSW 2 124664162 missense probably damaging 1.00
R4599:Sema6d UTSW 2 124654231 missense probably damaging 1.00
R4822:Sema6d UTSW 2 124662294 missense possibly damaging 0.79
R4884:Sema6d UTSW 2 124656818 splice site probably null
R5288:Sema6d UTSW 2 124664246 missense probably damaging 1.00
R5443:Sema6d UTSW 2 124656836 missense probably damaging 1.00
R5504:Sema6d UTSW 2 124658021 missense probably damaging 1.00
R5534:Sema6d UTSW 2 124659815 missense possibly damaging 0.75
R5615:Sema6d UTSW 2 124656901 missense probably damaging 0.97
R5747:Sema6d UTSW 2 124664947 missense probably damaging 0.99
R5866:Sema6d UTSW 2 124664342 missense probably benign 0.26
R5980:Sema6d UTSW 2 124664708 missense probably damaging 1.00
R6670:Sema6d UTSW 2 124654842 small deletion probably benign
R6803:Sema6d UTSW 2 124664050 missense probably damaging 0.96
R7023:Sema6d UTSW 2 124664911 missense probably damaging 1.00
R7068:Sema6d UTSW 2 124657821 missense probably benign
R7426:Sema6d UTSW 2 124654158 missense probably damaging 1.00
R7556:Sema6d UTSW 2 124654189 missense probably damaging 1.00
R7569:Sema6d UTSW 2 124657972 missense possibly damaging 0.92
Predicted Primers PCR Primer
(F):5'- ACAGGGGCGAAGGTGGACTATATTC -3'
(R):5'- TCGTTTCCGGCAAGTACACAGAAG -3'

Sequencing Primer
(F):5'- TGGACTATATTCAGGGGACACC -3'
(R):5'- GCAAGTTCTGGTGTTACCAAAG -3'
Posted On2013-06-12