Incidental Mutation 'R1889:Sema3d'
ID 209810
Institutional Source Beutler Lab
Gene Symbol Sema3d
Ensembl Gene ENSMUSG00000040254
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
Synonyms 4631426B19Rik
MMRRC Submission 039910-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # R1889 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 12433352-12638915 bp(+) (GRCm39)
Type of Mutation splice site (4 bp from exon)
DNA Base Change (assembly) A to G at 12534988 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000142453 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927] [ENSMUST00000197927]
AlphaFold Q8BH34
Predicted Effect probably null
Transcript: ENSMUST00000030868
SMART Domains Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254

DomainStartEndE-ValueType
transmembrane domain 16 35 N/A INTRINSIC
Sema 70 515 2.97e-207 SMART
PSI 533 585 2.03e-13 SMART
IG 598 682 1.39e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196093
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196618
Predicted Effect probably null
Transcript: ENSMUST00000197927
SMART Domains Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254

DomainStartEndE-ValueType
signal peptide 1 37 N/A INTRINSIC
Sema 70 515 1e-209 SMART
PSI 533 585 8.5e-16 SMART
Blast:Sema 590 622 1e-9 BLAST
Predicted Effect probably null
Transcript: ENSMUST00000197927
SMART Domains Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254

DomainStartEndE-ValueType
signal peptide 1 37 N/A INTRINSIC
Sema 70 515 1e-209 SMART
PSI 533 585 8.5e-16 SMART
Blast:Sema 590 622 1e-9 BLAST
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 97.1%
  • 3x: 96.2%
  • 10x: 93.6%
  • 20x: 88.0%
Validation Efficiency 97% (103/106)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 86 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579C12Rik A G 9: 89,034,815 (GRCm39) noncoding transcript Het
9130008F23Rik T C 17: 41,191,193 (GRCm39) R79G probably damaging Het
Aco1 A T 4: 40,164,607 (GRCm39) probably null Het
Acp6 C T 3: 97,073,201 (GRCm39) R81W probably damaging Het
Agbl1 A C 7: 76,239,129 (GRCm39) Y543S probably damaging Het
Anapc7 T C 5: 122,571,539 (GRCm39) W205R probably damaging Het
Ap1g2 T A 14: 55,338,886 (GRCm39) M532L probably damaging Het
Appl1 A G 14: 26,647,470 (GRCm39) probably benign Het
Arhgef19 T C 4: 140,976,624 (GRCm39) F462S probably damaging Het
Astn1 A G 1: 158,332,886 (GRCm39) probably null Het
AU015836 T C X: 93,012,985 (GRCm39) probably benign Het
Cacna1c C T 6: 118,589,586 (GRCm39) R1446H probably damaging Het
Cadm2 T C 16: 66,679,683 (GRCm39) D50G probably damaging Het
Ccdc81 G A 7: 89,531,502 (GRCm39) Q324* probably null Het
Cd300lf A G 11: 115,011,206 (GRCm39) V178A probably benign Het
Cdt1 T C 8: 123,298,791 (GRCm39) V476A possibly damaging Het
Cenpj A G 14: 56,796,182 (GRCm39) V225A probably benign Het
Cep295 T C 9: 15,243,399 (GRCm39) T1686A possibly damaging Het
Cfap54 A G 10: 92,870,572 (GRCm39) S684P possibly damaging Het
Clip1 C A 5: 123,791,559 (GRCm39) V204F probably damaging Het
Cnpy4 A G 5: 138,191,102 (GRCm39) E226G probably benign Het
Col6a3 T A 1: 90,731,433 (GRCm39) M1000L probably benign Het
Cpsf1 T C 15: 76,486,356 (GRCm39) M335V probably benign Het
Dnmt3b C A 2: 153,518,679 (GRCm39) A614E probably benign Het
Dpm1 C T 2: 168,059,655 (GRCm39) R147Q possibly damaging Het
Dpp7 G T 2: 25,243,691 (GRCm39) probably null Het
Engase T C 11: 118,369,759 (GRCm39) F57S probably damaging Het
Epb41l5 T C 1: 119,476,902 (GRCm39) D718G possibly damaging Het
Fam20a T C 11: 109,564,380 (GRCm39) K458E probably benign Het
Fbxo44 C G 4: 148,240,726 (GRCm39) R220S probably damaging Het
Gkn2 T A 6: 87,355,137 (GRCm39) Y115* probably null Het
Gtdc1 A G 2: 44,481,926 (GRCm39) S246P probably damaging Het
H2-Q2 A G 17: 35,564,152 (GRCm39) D302G probably benign Het
Herc2 C T 7: 55,839,561 (GRCm39) S3357L possibly damaging Het
Herc6 T A 6: 57,639,060 (GRCm39) Y840* probably null Het
Hoxa10 GGCTGCTGCTGCTGCTGCTG GGCTGCTGCTGCTGCTG 6: 52,211,472 (GRCm39) probably benign Het
Ift122 T C 6: 115,871,382 (GRCm39) probably null Het
Ilf3 T A 9: 21,316,063 (GRCm39) probably benign Het
Itgb2 A T 10: 77,384,457 (GRCm39) N193Y possibly damaging Het
Itgb5 T G 16: 33,730,839 (GRCm39) I65S probably damaging Het
Jpt2 T C 17: 25,179,585 (GRCm39) M1V probably null Het
Kcnt2 A T 1: 140,512,031 (GRCm39) H995L probably damaging Het
Kif20b T C 19: 34,918,608 (GRCm39) probably benign Het
Kif7 T C 7: 79,360,211 (GRCm39) Y342C probably damaging Het
Klhl21 T C 4: 152,099,877 (GRCm39) V529A possibly damaging Het
Klhl26 T C 8: 70,904,383 (GRCm39) D475G probably damaging Het
Lcor T C 19: 41,547,567 (GRCm39) Y384H probably damaging Het
Lrp1b A T 2: 40,809,179 (GRCm39) C2463* probably null Het
Marchf6 T C 15: 31,459,339 (GRCm39) E909G possibly damaging Het
Mrc1 A T 2: 14,313,488 (GRCm39) probably null Het
Mtrex T C 13: 113,024,024 (GRCm39) N707S probably benign Het
Nipal4 T A 11: 46,041,560 (GRCm39) I212F probably damaging Het
Nup98 T A 7: 101,809,923 (GRCm39) T536S probably damaging Het
Nwd2 A G 5: 63,965,009 (GRCm39) E1531G possibly damaging Het
Nxpe2 T C 9: 48,237,914 (GRCm39) T114A probably damaging Het
Oosp1 C T 19: 11,645,158 (GRCm39) V169I possibly damaging Het
Opa1 T C 16: 29,444,403 (GRCm39) V863A possibly damaging Het
Or5ac22 T G 16: 59,135,326 (GRCm39) Y148S probably damaging Het
Pabpc4l A T 3: 46,400,798 (GRCm39) M282K probably benign Het
Parp14 G A 16: 35,677,130 (GRCm39) A946V probably benign Het
Pcnx3 T C 19: 5,722,684 (GRCm39) D1336G probably damaging Het
Phlpp1 T C 1: 106,246,580 (GRCm39) V590A possibly damaging Het
Rbck1 T A 2: 152,160,276 (GRCm39) T468S probably damaging Het
Ripor2 T A 13: 24,877,870 (GRCm39) I290N probably damaging Het
Rnf139 T C 15: 58,771,346 (GRCm39) L457P probably damaging Het
Rtn1 C A 12: 72,351,184 (GRCm39) A342S possibly damaging Het
Serpinb2 T A 1: 107,452,337 (GRCm39) V305D probably damaging Het
Sez6l2 T C 7: 126,552,668 (GRCm39) V148A probably damaging Het
Shank2 C A 7: 143,740,595 (GRCm39) S568* probably null Het
Slc10a4 T C 5: 73,169,490 (GRCm39) S372P possibly damaging Het
Slc10a5 T C 3: 10,400,550 (GRCm39) T37A probably benign Het
Slc14a1 T C 18: 78,152,912 (GRCm39) I276V possibly damaging Het
Slc6a20b G T 9: 123,461,269 (GRCm39) D52E probably benign Het
Slc6a5 T C 7: 49,601,182 (GRCm39) M661T probably benign Het
Ssh2 C G 11: 77,340,571 (GRCm39) D574E probably damaging Het
Steap4 G T 5: 8,025,892 (GRCm39) R151L probably damaging Het
Sun5 T A 2: 153,707,915 (GRCm39) I107L probably benign Het
Tacc1 C T 8: 25,665,269 (GRCm39) V488M probably damaging Het
Tgs1 A G 4: 3,614,928 (GRCm39) T829A probably benign Het
Tnxb A G 17: 34,914,799 (GRCm39) E1929G probably damaging Het
Tssc4 A C 7: 142,624,292 (GRCm39) Q200P probably damaging Het
Ttn A G 2: 76,588,876 (GRCm39) W21398R probably damaging Het
Usp50 C T 2: 126,619,818 (GRCm39) probably null Het
Usp9y A T Y: 1,448,829 (GRCm39) probably null Het
V1rd19 T A 7: 23,702,632 (GRCm39) F33I probably benign Het
Zfat T C 15: 67,973,388 (GRCm39) T1118A probably benign Het
Other mutations in Sema3d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00559:Sema3d APN 5 12,613,189 (GRCm39) missense probably benign 0.01
IGL00582:Sema3d APN 5 12,635,162 (GRCm39) missense probably damaging 1.00
IGL00661:Sema3d APN 5 12,555,806 (GRCm39) missense probably damaging 1.00
IGL00780:Sema3d APN 5 12,574,293 (GRCm39) missense probably damaging 1.00
IGL01531:Sema3d APN 5 12,591,047 (GRCm39) missense probably benign
IGL01957:Sema3d APN 5 12,613,282 (GRCm39) missense probably damaging 1.00
IGL02100:Sema3d APN 5 12,634,958 (GRCm39) missense probably benign 0.29
IGL02676:Sema3d APN 5 12,620,945 (GRCm39) missense probably benign 0.38
IGL02749:Sema3d APN 5 12,613,112 (GRCm39) splice site probably benign
IGL02827:Sema3d APN 5 12,635,085 (GRCm39) missense probably benign 0.04
IGL03325:Sema3d APN 5 12,513,189 (GRCm39) missense probably damaging 0.99
R0050:Sema3d UTSW 5 12,634,920 (GRCm39) missense probably benign 0.00
R0085:Sema3d UTSW 5 12,620,953 (GRCm39) missense probably benign 0.00
R0095:Sema3d UTSW 5 12,613,314 (GRCm39) missense probably damaging 1.00
R0157:Sema3d UTSW 5 12,558,104 (GRCm39) missense possibly damaging 0.95
R0328:Sema3d UTSW 5 12,498,042 (GRCm39) missense possibly damaging 0.48
R0924:Sema3d UTSW 5 12,513,183 (GRCm39) missense possibly damaging 0.69
R0930:Sema3d UTSW 5 12,513,183 (GRCm39) missense possibly damaging 0.69
R1609:Sema3d UTSW 5 12,591,023 (GRCm39) missense probably damaging 1.00
R1657:Sema3d UTSW 5 12,634,941 (GRCm39) missense possibly damaging 0.82
R1669:Sema3d UTSW 5 12,558,051 (GRCm39) splice site probably benign
R1795:Sema3d UTSW 5 12,634,854 (GRCm39) missense probably benign 0.02
R1861:Sema3d UTSW 5 12,547,570 (GRCm39) missense probably benign 0.00
R1895:Sema3d UTSW 5 12,623,810 (GRCm39) missense probably damaging 1.00
R1946:Sema3d UTSW 5 12,623,810 (GRCm39) missense probably damaging 1.00
R1975:Sema3d UTSW 5 12,634,965 (GRCm39) missense probably benign
R1975:Sema3d UTSW 5 12,613,285 (GRCm39) missense probably damaging 1.00
R2117:Sema3d UTSW 5 12,613,240 (GRCm39) missense probably benign
R2148:Sema3d UTSW 5 12,534,926 (GRCm39) missense probably damaging 0.99
R2276:Sema3d UTSW 5 12,592,549 (GRCm39) missense possibly damaging 0.63
R3761:Sema3d UTSW 5 12,621,004 (GRCm39) missense probably damaging 1.00
R4063:Sema3d UTSW 5 12,635,091 (GRCm39) missense probably benign 0.25
R4428:Sema3d UTSW 5 12,498,087 (GRCm39) missense probably benign 0.32
R4903:Sema3d UTSW 5 12,613,125 (GRCm39) missense probably benign 0.00
R4999:Sema3d UTSW 5 12,558,054 (GRCm39) splice site probably null
R5000:Sema3d UTSW 5 12,498,005 (GRCm39) missense probably benign 0.01
R5022:Sema3d UTSW 5 12,634,923 (GRCm39) missense probably damaging 1.00
R5186:Sema3d UTSW 5 12,634,875 (GRCm39) missense probably benign
R5584:Sema3d UTSW 5 12,620,954 (GRCm39) missense possibly damaging 0.73
R5584:Sema3d UTSW 5 12,615,975 (GRCm39) missense possibly damaging 0.49
R6270:Sema3d UTSW 5 12,498,074 (GRCm39) missense probably benign
R6368:Sema3d UTSW 5 12,620,980 (GRCm39) missense probably damaging 1.00
R6426:Sema3d UTSW 5 12,613,231 (GRCm39) missense probably damaging 1.00
R6750:Sema3d UTSW 5 12,635,067 (GRCm39) nonsense probably null
R7403:Sema3d UTSW 5 12,547,551 (GRCm39) missense probably damaging 0.97
R7450:Sema3d UTSW 5 12,634,901 (GRCm39) nonsense probably null
R7470:Sema3d UTSW 5 12,558,152 (GRCm39) missense probably damaging 1.00
R7548:Sema3d UTSW 5 12,627,783 (GRCm39) missense unknown
R7593:Sema3d UTSW 5 12,558,112 (GRCm39) missense probably benign 0.02
R7683:Sema3d UTSW 5 12,623,823 (GRCm39) nonsense probably null
R8155:Sema3d UTSW 5 12,498,148 (GRCm39) critical splice donor site probably null
R8442:Sema3d UTSW 5 12,592,608 (GRCm39) missense probably damaging 0.99
R8725:Sema3d UTSW 5 12,555,822 (GRCm39) missense probably damaging 1.00
R8754:Sema3d UTSW 5 12,603,191 (GRCm39) critical splice donor site probably null
R9293:Sema3d UTSW 5 12,603,181 (GRCm39) missense probably damaging 1.00
R9771:Sema3d UTSW 5 12,613,207 (GRCm39) missense probably damaging 0.99
Z1176:Sema3d UTSW 5 12,635,026 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TCCAAAGCCGTGGTTGATG -3'
(R):5'- AAATCCAACCTCAGCTCAGGTG -3'

Sequencing Primer
(F):5'- CCAAAGCCGTGGTTGATGTCTAC -3'
(R):5'- CACTACGTTGCAGAAGCTAGCTTTG -3'
Posted On 2014-06-30