Incidental Mutation 'R5443:Sema6d'
ID 427258
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 043008-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5443 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 123931889-124509690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 124498756 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 222 (H222L)
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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: H222L

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: H222L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: H222L

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 0.2383 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.9%
Validation Efficiency 99% (68/69)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap12 A T 10: 4,305,576 (GRCm39) E795D probably damaging Het
Aldh6a1 T C 12: 84,484,745 (GRCm39) probably null Het
Aox4 A G 1: 58,273,151 (GRCm39) probably null Het
Arhgap39 G A 15: 76,682,125 (GRCm39) probably benign Het
AW551984 T C 9: 39,509,325 (GRCm39) E272G possibly damaging Het
C1qc G A 4: 136,619,804 (GRCm39) probably benign Het
Carhsp1 C A 16: 8,482,203 (GRCm39) R26L probably benign Het
Cdh12 G T 15: 21,237,935 (GRCm39) V57L probably benign Het
Cfap298 G T 16: 90,724,099 (GRCm39) Q168K probably benign Het
Clec3a A G 8: 115,144,893 (GRCm39) Y23C probably benign Het
Crebrf G C 17: 26,961,328 (GRCm39) V150L probably damaging Het
Ddx41 G T 13: 55,683,104 (GRCm39) A201E probably benign Het
Doc2b T C 11: 75,670,921 (GRCm39) K237E probably damaging Het
Dst T C 1: 34,267,620 (GRCm39) S5199P probably damaging Het
Efnb2 A G 8: 8,670,862 (GRCm39) I129T probably damaging Het
Epg5 A G 18: 78,070,712 (GRCm39) E2329G possibly damaging Het
Esrrg A C 1: 187,775,622 (GRCm39) T27P possibly damaging Het
Fah T A 7: 84,241,604 (GRCm39) R316W probably damaging Het
Fat4 T C 3: 39,064,519 (GRCm39) L4825P probably damaging Het
Gabbr1 T C 17: 37,381,648 (GRCm39) V804A probably damaging Het
Gm1322 G A 2: 67,015,012 (GRCm39) noncoding transcript Het
Gm5114 T A 7: 39,058,289 (GRCm39) K443N probably benign Het
Gnai2 T C 9: 107,497,386 (GRCm39) I3V probably damaging Het
Gp2 G A 7: 119,053,821 (GRCm39) P47S possibly damaging Het
Klf15 C A 6: 90,444,342 (GRCm39) Q306K possibly damaging Het
Ly6a2 A T 15: 75,005,568 (GRCm39) noncoding transcript Het
Maco1 A T 4: 134,560,619 (GRCm39) C121* probably null Het
Necab2 A T 8: 120,195,032 (GRCm39) M295L probably benign Het
Nrg1 A T 8: 32,339,348 (GRCm39) Y208N probably damaging Het
Nup88 A T 11: 70,849,256 (GRCm39) Y232* probably null Het
Oacyl A G 18: 65,883,253 (GRCm39) R611G probably benign Het
Oasl1 T C 5: 115,074,129 (GRCm39) probably null Het
Or2n1e T A 17: 38,585,905 (GRCm39) M81K probably damaging Het
Or2y14 G T 11: 49,405,262 (GRCm39) G266C probably damaging Het
Or52h7 T C 7: 104,213,583 (GRCm39) Y52H probably benign Het
Or8k25 A C 2: 86,243,937 (GRCm39) I153R possibly damaging Het
Pate4 A C 9: 35,519,170 (GRCm39) S66A possibly damaging Het
Pigl T A 11: 62,349,309 (GRCm39) C8* probably null Het
Plg G A 17: 12,601,070 (GRCm39) A51T probably benign Het
Polr3a T C 14: 24,505,009 (GRCm39) I1084V possibly damaging Het
Ppig A T 2: 69,564,635 (GRCm39) D97V probably damaging Het
Ppp1r16a A G 15: 76,578,846 (GRCm39) K517E possibly damaging Het
Prr16 A T 18: 51,436,225 (GRCm39) S235C probably damaging Het
Psmd1 G A 1: 86,017,905 (GRCm39) R572H probably damaging Het
Sbf2 T C 7: 109,977,135 (GRCm39) probably benign Het
Scrt2 A T 2: 151,924,043 (GRCm39) Y25F probably benign Het
Septin2 A G 1: 93,425,174 (GRCm39) N110S possibly damaging Het
Shpk G A 11: 73,113,607 (GRCm39) G340D possibly damaging Het
Smg5 T A 3: 88,261,896 (GRCm39) L723H probably damaging Het
Sp110 C T 1: 85,516,841 (GRCm39) E219K possibly damaging Het
Spo11 T C 2: 172,831,152 (GRCm39) probably benign Het
Srarp T A 4: 141,163,388 (GRCm39) probably null Het
Tbc1d5 A G 17: 51,042,995 (GRCm39) I831T probably damaging Het
Tm9sf2 A T 14: 122,363,607 (GRCm39) Y109F probably damaging Het
Tpcn2 A T 7: 144,809,209 (GRCm39) M699K possibly damaging Het
Trim34a T C 7: 103,909,420 (GRCm39) F289S possibly damaging Het
Trim39 T C 17: 36,571,645 (GRCm39) H371R probably damaging Het
Usp48 T A 4: 137,348,532 (GRCm39) I11N possibly damaging Het
Zbtb10 T C 3: 9,345,108 (GRCm39) F677L probably benign Het
Zer1 C T 2: 30,001,008 (GRCm39) G138S probably damaging Het
Zfp612 A G 8: 110,816,227 (GRCm39) K439R possibly 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
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'- ACCTTTGCTGTAGCTCAGTTCG -3'
(R):5'- CTTTGAAACAGCACAGGAGAGC -3'

Sequencing Primer
(F):5'- TAGCTCAGTTCGCTGCAG -3'
(R):5'- GGAGAGCACCCATCACCCTTC -3'
Posted On 2016-09-01