Incidental Mutation 'R8155:Sema3d'
ID 633249
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 067581-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # R8155 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 12433352-12638915 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 12498148 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000030868 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868] [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 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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.8%
  • 10x: 99.5%
  • 20x: 98.9%
Validation Efficiency 100% (62/62)
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 G A 1: 71,330,497 (GRCm39) T1386I probably damaging Het
Abcb6 A T 1: 75,151,413 (GRCm39) V504E probably damaging Het
Abtb3 G A 10: 85,476,473 (GRCm39) probably null Het
Adprhl1 C T 8: 13,271,764 (GRCm39) A1665T probably damaging Het
Arhgap32 T A 9: 32,093,196 (GRCm39) L183H probably damaging Het
Arhgef12 A G 9: 42,953,958 (GRCm39) L24S probably damaging Het
B3gnt4 C T 5: 123,649,426 (GRCm39) H264Y possibly damaging Het
Cfi A G 3: 129,648,739 (GRCm39) T208A probably benign Het
Chd4 T A 6: 125,082,287 (GRCm39) F605Y probably benign Het
Cimap1d A T 10: 79,481,466 (GRCm39) V21E probably benign Het
Clip1 A G 5: 123,751,699 (GRCm39) L694P Het
Crybb3 A T 5: 113,225,466 (GRCm39) D135E probably damaging Het
Ddx60 T A 8: 62,470,205 (GRCm39) S1398T possibly damaging Het
Dusp5 T A 19: 53,529,537 (GRCm39) Y313* probably null Het
Eloa A G 4: 135,734,438 (GRCm39) V689A probably benign Het
Ep300 T A 15: 81,505,269 (GRCm39) Y630N unknown Het
Galnt5 A T 2: 57,889,427 (GRCm39) K342N probably benign Het
Gm4841 A G 18: 60,403,409 (GRCm39) V228A probably damaging Het
Gna14 A T 19: 16,576,338 (GRCm39) D115V probably benign Het
Gpx5 T C 13: 21,472,917 (GRCm39) D139G probably damaging Het
Hmcn1 G T 1: 150,480,705 (GRCm39) N4490K probably damaging Het
Hsp90aa1 T C 12: 110,661,828 (GRCm39) S63G unknown Het
Itpkb T C 1: 180,159,913 (GRCm39) I13T possibly damaging Het
Itprid2 T C 2: 79,475,177 (GRCm39) S379P probably benign Het
Lamb2 C T 9: 108,357,845 (GRCm39) R123W probably damaging Het
Ldha A G 7: 46,503,508 (GRCm39) H300R probably damaging Het
Lrp2 A G 2: 69,313,342 (GRCm39) L2463P possibly damaging Het
Morf4l1 A G 9: 89,977,225 (GRCm39) I232T probably damaging Het
Mtg1 A G 7: 139,724,622 (GRCm39) H166R probably benign Het
Or14a260 A G 7: 85,985,386 (GRCm39) S73P probably damaging Het
Or2ad1 A G 13: 21,327,062 (GRCm39) L55P probably damaging Het
Or52r1 C T 7: 102,536,452 (GRCm39) D303N probably benign Het
Or5d46 A G 2: 88,170,296 (GRCm39) N129S probably damaging Het
Or6d12 T A 6: 116,492,813 (GRCm39) V25E probably benign Het
Or7g32 A T 9: 19,389,453 (GRCm39) V31D probably benign Het
Papss2 A G 19: 32,618,742 (GRCm39) T267A probably benign Het
Park7 G A 4: 150,991,547 (GRCm39) R48C possibly damaging Het
Pecr A G 1: 72,309,443 (GRCm39) V199A probably damaging Het
Pla2g10 G A 16: 13,543,048 (GRCm39) R80W probably damaging Het
Plek2 G A 12: 78,943,066 (GRCm39) R77* probably null Het
Psg23 A G 7: 18,346,179 (GRCm39) L172P probably damaging Het
Psg25 A C 7: 18,260,445 (GRCm39) F151C probably benign Het
Ptpn3 G T 4: 57,232,336 (GRCm39) H433Q probably benign Het
Rasal3 A G 17: 32,616,381 (GRCm39) V294A possibly damaging Het
Rnf6 T C 5: 146,147,815 (GRCm39) D401G probably damaging Het
Rsf1 GCG GCGACG 7: 97,229,114 (GRCm39) probably benign Het
Serpinb1c A T 13: 33,081,038 (GRCm39) L15Q probably damaging Het
Slfn3 T A 11: 83,103,611 (GRCm39) Y161N probably damaging Het
Spns2 T C 11: 72,347,394 (GRCm39) M404V possibly damaging Het
Stk39 T A 2: 68,097,410 (GRCm39) I479L probably damaging Het
Tbx15 C A 3: 99,259,886 (GRCm39) Q586K possibly damaging Het
Thap11 C T 8: 106,582,854 (GRCm39) R288* probably null Het
Tm7sf2 T A 19: 6,114,125 (GRCm39) D236V probably damaging Het
Tmem214 T C 5: 31,029,136 (GRCm39) S192P possibly damaging Het
Tnfaip3 A G 10: 18,880,439 (GRCm39) S543P possibly damaging Het
Traf3ip3 A G 1: 192,860,524 (GRCm39) L466P probably damaging Het
Tspan18 C T 2: 93,040,357 (GRCm39) probably null Het
Vmn1r229 T A 17: 21,035,472 (GRCm39) L239Q probably damaging Het
Vsig2 T C 9: 37,455,329 (GRCm39) V293A possibly damaging Het
Wdfy4 A T 14: 32,884,776 (GRCm39) V42D Het
Wnk2 G A 13: 49,192,577 (GRCm39) P2055S unknown Het
Zfp953 C A 13: 67,491,535 (GRCm39) C139F probably damaging 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
R1889:Sema3d UTSW 5 12,534,988 (GRCm39) splice site probably null
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
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'- TCCTCATTAAGGGTGAACTAACAG -3'
(R):5'- TCTCAGCTATTGTAGACTGTGAAAC -3'

Sequencing Primer
(F):5'- CATTAAGGGTGAACTAACAGTGTTTG -3'
(R):5'- GACTGTGAAACATTTTAGGTT -3'
Posted On 2020-06-30