Incidental Mutation 'R0269:Sema6d'
ID 35129
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 038495-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0269 (G1)
Quality Score 206
Status Validated
Chromosome 2
Chromosomal Location 123931889-124509690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 124502665 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 583 (F583L)
Ref Sequence ENSEMBL: ENSMUSP00000099529 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051419] [ENSMUST00000076335] [ENSMUST00000077847] [ENSMUST00000078621] [ENSMUST00000103238] [ENSMUST00000103239] [ENSMUST00000103240] [ENSMUST00000103241]
AlphaFold Q76KF0
Predicted Effect probably benign
Transcript: ENSMUST00000051419
SMART Domains Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200

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 benign
Transcript: ENSMUST00000076335
SMART Domains Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200

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 benign
Transcript: ENSMUST00000077847
SMART Domains Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200

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: F596L

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: F596L

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 benign
Transcript: ENSMUST00000103238
SMART Domains Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200

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 possibly damaging
Transcript: ENSMUST00000103239
AA Change: F583L

PolyPhen 2 Score 0.630 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: F583L

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: F583L

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: F583L

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 noncoding transcript
Transcript: ENSMUST00000132088
Predicted Effect probably benign
Transcript: ENSMUST00000103241
SMART Domains Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200

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
Meta Mutation Damage Score 0.0704 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.8%
  • 10x: 96.1%
  • 20x: 93.6%
Validation Efficiency 100% (59/59)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5031439G07Rik C T 15: 84,838,201 (GRCm39) V231I possibly damaging Het
Abca1 T C 4: 53,044,228 (GRCm39) D1798G probably benign Het
Adcy2 T A 13: 68,826,725 (GRCm39) K660* probably null Het
Alk G T 17: 72,910,578 (GRCm39) P43T probably damaging Het
Amhr2 T C 15: 102,355,503 (GRCm39) C189R probably benign Het
Arrb1 T C 7: 99,243,884 (GRCm39) L278P probably damaging Het
AW551984 T C 9: 39,511,246 (GRCm39) Y153C probably damaging Het
Bpifb1 A G 2: 154,054,867 (GRCm39) D253G possibly damaging Het
Bpifb9b C T 2: 154,161,545 (GRCm39) T559M probably benign Het
Cd46 T G 1: 194,746,996 (GRCm39) I339L probably benign Het
Cdkn2aip A G 8: 48,165,012 (GRCm39) S234P probably damaging Het
Chil3 T C 3: 106,063,072 (GRCm39) K173E probably benign Het
Csf2rb2 G T 15: 78,173,065 (GRCm39) T265N probably benign Het
Cyp2c40 A G 19: 39,762,340 (GRCm39) F436L probably damaging Het
D130040H23Rik T C 8: 69,753,446 (GRCm39) F24S probably benign Het
Defb12 G T 8: 19,164,375 (GRCm39) A34E probably damaging Het
Fam234a A T 17: 26,435,591 (GRCm39) D264E probably benign Het
Fbxl17 A C 17: 63,691,987 (GRCm39) F42V probably damaging Het
Gldc T A 19: 30,096,002 (GRCm39) I670F probably damaging Het
Guf1 A C 5: 69,716,942 (GRCm39) Q168P probably damaging Het
Hcn2 A G 10: 79,570,075 (GRCm39) probably benign Het
Hddc2 A G 10: 31,203,942 (GRCm39) M190V probably benign Het
Kcnq2 T C 2: 180,738,767 (GRCm39) E294G probably benign Het
Kdelr1 T A 7: 45,523,463 (GRCm39) probably benign Het
Kidins220 T A 12: 25,090,511 (GRCm39) H1158Q probably damaging Het
Laptm5 A T 4: 130,658,127 (GRCm39) N185Y probably benign Het
Mgat4a A G 1: 37,529,388 (GRCm39) Y164H possibly damaging Het
Mlh3 C A 12: 85,315,179 (GRCm39) V336L probably benign Het
Myadm A G 7: 3,345,273 (GRCm39) T12A unknown Het
Nol8 T C 13: 49,807,921 (GRCm39) F46L possibly damaging Het
Ntrk1 T C 3: 87,691,240 (GRCm39) D308G possibly damaging Het
Oog3 A T 4: 143,886,784 (GRCm39) V112D probably benign Het
Or4a66 A G 2: 88,531,040 (GRCm39) V211A probably damaging Het
Or5af2 T C 11: 58,707,975 (GRCm39) V47A probably damaging Het
Or5m9b A G 2: 85,905,485 (GRCm39) M134V probably benign Het
Or8g34 T C 9: 39,373,090 (GRCm39) M118T probably damaging Het
Or9s18 A T 13: 65,300,692 (GRCm39) Y218F possibly damaging Het
Pramel14 A G 4: 143,720,088 (GRCm39) probably benign Het
Prss39 A T 1: 34,539,279 (GRCm39) H173L probably damaging Het
Rabl6 A G 2: 25,476,878 (GRCm39) probably null Het
Recql5 T C 11: 115,819,050 (GRCm39) D172G possibly damaging Het
Reln T C 5: 22,125,535 (GRCm39) D2716G probably damaging Het
Rgs7 A G 1: 175,098,386 (GRCm39) S58P possibly damaging Het
Sgsm1 T C 5: 113,434,795 (GRCm39) probably null Het
Slc22a19 A T 19: 7,686,986 (GRCm39) probably benign Het
Slc6a21 T A 7: 44,936,332 (GRCm39) Y428* probably null Het
Smarca4 T G 9: 21,547,497 (GRCm39) M260R probably benign Het
Smg6 C A 11: 75,053,757 (GRCm39) T1413K probably benign Het
Spata17 T C 1: 186,830,069 (GRCm39) I322V probably benign Het
Stxbp1 A C 2: 32,692,795 (GRCm39) I407S probably damaging Het
Sult1d1 A T 5: 87,712,661 (GRCm39) I61N probably damaging Het
Sytl2 T C 7: 90,052,228 (GRCm39) probably benign Het
Tm4sf5 T A 11: 70,401,495 (GRCm39) S165T probably damaging Het
Tmx2 T C 2: 84,502,740 (GRCm39) D256G probably benign Het
Trmt11 T A 10: 30,463,485 (GRCm39) H210L probably benign Het
Tut7 A T 13: 59,964,669 (GRCm39) probably null Het
Ush2a T A 1: 188,542,373 (GRCm39) M3313K probably benign Het
Zfp955b A T 17: 33,524,437 (GRCm39) S43R probably damaging 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
R0390:Sema6d UTSW 2 124,500,410 (GRCm39) missense probably damaging 1.00
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'- GCAGCCTTGATAATGACTCGGGAC -3'
(R):5'- TGAACCATTCCATGCTACACACGG -3'

Sequencing Primer
(F):5'- CTTGATAATGACTCGGGACACATAG -3'
(R):5'- GGCTGAGTAAGAAAACATCTCTC -3'
Posted On 2013-05-09