Incidental Mutation 'R7569:Sema6d'
ID 585622
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 045657-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7569 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 123931889-124509690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 124499892 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 323 (I323V)
Ref Sequence ENSEMBL: ENSMUSP00000061123 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051419] [ENSMUST00000076335] [ENSMUST00000077847] [ENSMUST00000078621] [ENSMUST00000103238] [ENSMUST00000103239] [ENSMUST00000103240] [ENSMUST00000103241]
AlphaFold Q76KF0
Predicted Effect possibly damaging
Transcript: ENSMUST00000051419
AA Change: I323V

PolyPhen 2 Score 0.916 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: I323V

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: I323V

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: I323V

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 possibly damaging
Transcript: ENSMUST00000077847
AA Change: I323V

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: I323V

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: I323V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: I323V

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 possibly damaging
Transcript: ENSMUST00000103238
AA Change: I323V

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: I323V

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: I323V

PolyPhen 2 Score 0.825 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: I323V

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: I323V

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: I323V

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: I323V

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: I323V

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 0.3495 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 98% (58/59)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330182O14Rik A T 15: 40,008,344 (GRCm39) T73S unknown Het
Acvrl1 A G 15: 101,033,636 (GRCm39) Q106R probably benign Het
Adgb A T 10: 10,306,996 (GRCm39) D329E probably benign Het
Ankrd12 A T 17: 66,289,900 (GRCm39) D1844E probably damaging Het
Ankub1 G A 3: 57,573,039 (GRCm39) R228* probably null Het
Apol6 A C 15: 76,934,898 (GRCm39) probably benign Het
Ascc2 G A 11: 4,629,506 (GRCm39) V618M probably damaging Het
Asic3 A G 5: 24,619,046 (GRCm39) T113A probably benign Het
BC034090 T A 1: 155,093,151 (GRCm39) H769L probably benign Het
Bcl11a G T 11: 24,035,458 (GRCm39) E65* probably null Het
Birc6 G T 17: 74,905,077 (GRCm39) R1290L possibly damaging Het
C6 A G 15: 4,819,063 (GRCm39) E465G probably benign Het
Cav2 T A 6: 17,282,078 (GRCm39) I112N probably damaging Het
Cep131 G A 11: 119,957,539 (GRCm39) A848V probably damaging Het
Col8a1 T A 16: 57,447,555 (GRCm39) I652F unknown Het
Cul4a A G 8: 13,173,493 (GRCm39) N180S probably benign Het
Dhx38 A G 8: 110,287,327 (GRCm39) S214P probably damaging Het
Dmxl2 A G 9: 54,323,271 (GRCm39) V1197A possibly damaging Het
Dynlt1f A G 17: 6,923,181 (GRCm39) S7P not run Het
Eef1ece2 T A 16: 20,461,237 (GRCm39) Y641* probably null Het
Epha1 T A 6: 42,342,356 (GRCm39) T331S possibly damaging Het
Hus1b A G 13: 31,130,847 (GRCm39) Y271H probably damaging Het
Kmt2b A G 7: 30,268,978 (GRCm39) V2610A possibly damaging Het
Lama2 A G 10: 27,141,046 (GRCm39) L651P probably damaging Het
Lgr5 T C 10: 115,298,661 (GRCm39) Y361C probably damaging Het
Map1s T C 8: 71,366,142 (GRCm39) V349A probably benign Het
Map3k6 A G 4: 132,977,388 (GRCm39) R912G probably benign Het
Mtarc2 A T 1: 184,573,622 (GRCm39) F92Y possibly damaging Het
Nampt T A 12: 32,900,433 (GRCm39) H459Q probably benign Het
Nlrp1a T C 11: 70,999,869 (GRCm39) M817V probably benign Het
Npsr1 A G 9: 24,225,026 (GRCm39) R345G probably benign Het
Nuak2 G A 1: 132,244,019 (GRCm39) A18T possibly damaging Het
Or4d6 T C 19: 12,086,385 (GRCm39) D175G possibly damaging Het
Or5ak23 A G 2: 85,244,479 (GRCm39) V248A probably damaging Het
Pierce1 TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC 2: 28,356,122 (GRCm39) probably benign Het
Ppp4r3b T C 11: 29,138,540 (GRCm39) F296S possibly damaging Het
Pramel51 A T 12: 88,143,085 (GRCm39) Y373N probably benign Het
Pycr2 T C 1: 180,732,083 (GRCm39) F19L probably benign Het
Robo2 T A 16: 73,832,003 (GRCm39) T226S possibly damaging Het
Rock1 A T 18: 10,140,194 (GRCm39) N132K probably damaging Het
Rp1 A T 1: 4,355,063 (GRCm39) L379Q unknown Het
Slc12a4 A G 8: 106,672,479 (GRCm39) I814T probably damaging Het
Slc18a2 G A 19: 59,272,584 (GRCm39) G352R probably damaging Het
Slc39a14 T C 14: 70,547,276 (GRCm39) T357A possibly damaging Het
Smarcad1 T A 6: 65,029,695 (GRCm39) D94E probably benign Het
Sorcs2 A G 5: 36,183,220 (GRCm39) Y1018H probably benign Het
Srebf1 G T 11: 60,090,947 (GRCm39) T1069K possibly damaging Het
St3gal3 A G 4: 117,821,553 (GRCm39) V123A probably benign Het
Stradb A G 1: 59,030,310 (GRCm39) Y188C unknown Het
Styxl2 T C 1: 165,935,604 (GRCm39) D198G probably damaging Het
Sult2a2 T C 7: 13,513,430 (GRCm39) F186L probably benign Het
Syne2 A G 12: 75,974,164 (GRCm39) T1120A probably benign Het
Taok1 A T 11: 77,446,440 (GRCm39) S430T probably benign Het
Tmem62 A T 2: 120,837,411 (GRCm39) I573L probably benign Het
Trav9-1 T C 14: 53,725,581 (GRCm39) S7P probably benign Het
U2af1l4 A T 7: 30,262,982 (GRCm39) I24F probably damaging Het
Usp33 T A 3: 152,097,302 (GRCm39) I840N probably damaging Het
Vmn2r74 A C 7: 85,601,544 (GRCm39) I698S probably damaging Het
Zfp352 C T 4: 90,111,896 (GRCm39) P12L possibly damaging Het
Zfp507 T A 7: 35,493,969 (GRCm39) E358V 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
R0269:Sema6d UTSW 2 124,502,665 (GRCm39) missense possibly damaging 0.63
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
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'- TCGACGTCCTGCAGTCTATAAC -3'
(R):5'- AACATGTATTGGCCTCGGAGG -3'

Sequencing Primer
(F):5'- CAGACATAATCCAAATCAATGGCATC -3'
(R):5'- TGACAGATATTAAGATGGTCCTGATG -3'
Posted On 2019-10-17