Incidental Mutation 'R5264:Sema3e'
ID 401592
Institutional Source Beutler Lab
Gene Symbol Sema3e
Ensembl Gene ENSMUSG00000063531
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E
Synonyms Semah
MMRRC Submission 042832-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.509) question?
Stock # R5264 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 14075290-14306703 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 14276662 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 314 (L314F)
Ref Sequence ENSEMBL: ENSMUSP00000073612 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073957]
AlphaFold P70275
Predicted Effect probably damaging
Transcript: ENSMUST00000073957
AA Change: L314F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000073612
Gene: ENSMUSG00000063531
AA Change: L314F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 58 500 1.85e-194 SMART
PSI 518 573 1.81e-10 SMART
IG 587 673 5.75e-4 SMART
low complexity region 737 750 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130116
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199698
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.8%
Validation Efficiency 98% (54/55)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
PHENOTYPE: Homozygous null mice display abnormal intersomitic vacular development and loss of the normal segmented somite pattern. Homozygous mutants for another allele have Bergmeister papillae on the surface of the optic disc. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ckap2l A T 2: 129,127,299 (GRCm39) M293K probably benign Het
Col4a4 C T 1: 82,471,312 (GRCm39) G681E unknown Het
Dnai7 A G 6: 145,127,502 (GRCm39) V469A probably benign Het
Efcab7 G A 4: 99,735,372 (GRCm39) R132H probably benign Het
Elovl4 T C 9: 83,662,817 (GRCm39) T239A probably benign Het
Fank1 A G 7: 133,481,621 (GRCm39) D240G probably damaging Het
Fbln5 T A 12: 101,723,703 (GRCm39) M346L possibly damaging Het
Fbxl21 T C 13: 56,680,136 (GRCm39) F174L probably benign Het
Gns A G 10: 121,216,090 (GRCm39) D279G probably benign Het
Hmcn1 A G 1: 150,555,265 (GRCm39) V2502A probably benign Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Large2 A G 2: 92,205,088 (GRCm39) probably benign Het
Lrrc8b A T 5: 105,628,118 (GRCm39) I155F probably damaging Het
Morc2b T C 17: 33,357,353 (GRCm39) I140V probably benign Het
Mrgprb5 G A 7: 47,817,796 (GRCm39) S313L probably benign Het
Nectin4 A T 1: 171,211,273 (GRCm39) T266S probably benign Het
Nsd1 C T 13: 55,395,159 (GRCm39) A1023V possibly damaging Het
Or51a39 T C 7: 102,363,558 (GRCm39) T21A probably benign Het
Paqr8 A G 1: 21,005,332 (GRCm39) H162R possibly damaging Het
Pclo G A 5: 14,726,937 (GRCm39) probably benign Het
Phactr4 T C 4: 132,098,293 (GRCm39) D325G probably damaging Het
Plcg2 A T 8: 118,361,532 (GRCm39) E1255V possibly damaging Het
Polr3a T C 14: 24,505,009 (GRCm39) I1084V possibly damaging Het
Polr3b A T 10: 84,503,280 (GRCm39) Q399L probably benign Het
Ppp1r35 G A 5: 137,778,286 (GRCm39) probably benign Het
Psd3 A T 8: 68,166,377 (GRCm39) D919E probably benign Het
Ptgs2 A G 1: 149,978,481 (GRCm39) T198A possibly damaging Het
Ptpn14 T C 1: 189,564,997 (GRCm39) probably null Het
Ptprk A G 10: 28,461,582 (GRCm39) Y39C probably damaging Het
R3hdm4 A G 10: 79,749,175 (GRCm39) Y75H probably benign Het
Rsph4a A G 10: 33,785,379 (GRCm39) Y430C probably damaging Het
Samd12 C T 15: 53,723,669 (GRCm39) C8Y probably damaging Het
Sis A G 3: 72,857,089 (GRCm39) F401L probably damaging Het
Smoc1 T A 12: 81,151,474 (GRCm39) S64T probably damaging Het
Socs5 T A 17: 87,441,769 (GRCm39) H236Q probably damaging Het
Spaca1 C A 4: 34,049,863 (GRCm39) R45L possibly damaging Het
Spag6 A G 2: 18,750,324 (GRCm39) K457E probably benign Het
Stat2 T A 10: 128,116,934 (GRCm39) probably null Het
Tcp11l2 A G 10: 84,449,524 (GRCm39) I496M probably damaging Het
Ttll4 A G 1: 74,725,535 (GRCm39) I648V possibly damaging Het
Vmn2r67 T C 7: 84,801,453 (GRCm39) Y161C probably damaging Het
Wnt5b A T 6: 119,410,813 (GRCm39) V171E probably damaging Het
Zfp236 T C 18: 82,648,219 (GRCm39) K933E probably damaging Het
Zfp236 T C 18: 82,676,198 (GRCm39) E373G probably damaging Het
Zfp617 A G 8: 72,686,885 (GRCm39) Y405C probably damaging Het
Zranb1 CTGATGATGATG CTGATGATGATGATG 7: 132,584,556 (GRCm39) probably benign Het
Other mutations in Sema3e
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00503:Sema3e APN 5 14,290,586 (GRCm39) missense probably damaging 1.00
IGL01068:Sema3e APN 5 14,283,732 (GRCm39) critical splice donor site probably null
IGL01128:Sema3e APN 5 14,282,129 (GRCm39) missense probably damaging 1.00
IGL01134:Sema3e APN 5 14,302,784 (GRCm39) missense probably damaging 1.00
IGL02013:Sema3e APN 5 14,280,207 (GRCm39) missense probably damaging 1.00
IGL02051:Sema3e APN 5 14,274,324 (GRCm39) missense possibly damaging 0.77
IGL02309:Sema3e APN 5 14,274,404 (GRCm39) missense probably damaging 0.98
IGL02636:Sema3e APN 5 14,275,670 (GRCm39) missense probably benign
IGL02702:Sema3e APN 5 14,283,740 (GRCm39) splice site probably benign
IGL03001:Sema3e APN 5 14,291,057 (GRCm39) missense probably benign 0.19
R0011:Sema3e UTSW 5 14,194,025 (GRCm39) nonsense probably null
R0098:Sema3e UTSW 5 14,302,446 (GRCm39) missense possibly damaging 0.52
R0098:Sema3e UTSW 5 14,302,446 (GRCm39) missense possibly damaging 0.52
R0220:Sema3e UTSW 5 14,214,167 (GRCm39) missense possibly damaging 0.56
R0564:Sema3e UTSW 5 14,286,099 (GRCm39) critical splice donor site probably null
R1079:Sema3e UTSW 5 14,275,669 (GRCm39) missense probably benign 0.12
R1187:Sema3e UTSW 5 14,282,098 (GRCm39) missense probably damaging 1.00
R1670:Sema3e UTSW 5 14,212,199 (GRCm39) splice site probably benign
R1736:Sema3e UTSW 5 14,260,390 (GRCm39) missense probably damaging 1.00
R3433:Sema3e UTSW 5 14,302,728 (GRCm39) missense probably benign 0.00
R3831:Sema3e UTSW 5 14,276,496 (GRCm39) missense probably damaging 1.00
R4094:Sema3e UTSW 5 14,283,704 (GRCm39) missense probably benign 0.12
R4580:Sema3e UTSW 5 14,283,717 (GRCm39) missense probably damaging 1.00
R4828:Sema3e UTSW 5 14,276,654 (GRCm39) missense probably damaging 1.00
R4855:Sema3e UTSW 5 14,280,144 (GRCm39) missense probably damaging 0.99
R4884:Sema3e UTSW 5 14,275,579 (GRCm39) missense probably damaging 1.00
R4960:Sema3e UTSW 5 14,302,646 (GRCm39) missense possibly damaging 0.93
R5389:Sema3e UTSW 5 14,286,099 (GRCm39) critical splice donor site probably benign
R5512:Sema3e UTSW 5 14,280,194 (GRCm39) missense probably damaging 1.00
R5642:Sema3e UTSW 5 14,212,257 (GRCm39) missense probably damaging 1.00
R5647:Sema3e UTSW 5 14,275,567 (GRCm39) missense probably damaging 0.99
R5814:Sema3e UTSW 5 14,275,680 (GRCm39) missense probably benign 0.01
R5993:Sema3e UTSW 5 14,274,307 (GRCm39) missense probably damaging 1.00
R6076:Sema3e UTSW 5 14,291,100 (GRCm39) missense probably benign 0.01
R6906:Sema3e UTSW 5 14,290,601 (GRCm39) missense probably damaging 1.00
R7432:Sema3e UTSW 5 14,274,404 (GRCm39) missense probably damaging 0.98
R8738:Sema3e UTSW 5 14,214,169 (GRCm39) missense possibly damaging 0.95
R8849:Sema3e UTSW 5 14,302,673 (GRCm39) missense probably damaging 1.00
R8879:Sema3e UTSW 5 14,282,108 (GRCm39) missense probably benign 0.16
R8935:Sema3e UTSW 5 14,282,127 (GRCm39) missense probably damaging 0.97
R9071:Sema3e UTSW 5 14,282,154 (GRCm39) missense probably benign 0.00
R9100:Sema3e UTSW 5 14,282,208 (GRCm39) missense probably damaging 1.00
R9367:Sema3e UTSW 5 14,291,084 (GRCm39) missense probably benign 0.00
R9444:Sema3e UTSW 5 14,302,625 (GRCm39) missense possibly damaging 0.63
R9478:Sema3e UTSW 5 14,286,386 (GRCm39) missense probably damaging 1.00
R9601:Sema3e UTSW 5 14,302,397 (GRCm39) missense possibly damaging 0.95
R9671:Sema3e UTSW 5 14,212,217 (GRCm39) missense probably benign 0.00
X0064:Sema3e UTSW 5 14,280,156 (GRCm39) missense probably benign 0.05
Z1088:Sema3e UTSW 5 14,276,470 (GRCm39) missense probably damaging 0.97
Z1177:Sema3e UTSW 5 14,075,725 (GRCm39) start gained probably benign
Predicted Primers PCR Primer
(F):5'- CTGGTGAACAAGTGGAGCAC -3'
(R):5'- AGCCAGACACTTAAAGCTGC -3'

Sequencing Primer
(F):5'- GGAGCACTTTCCTTAAAGCG -3'
(R):5'- CCAGACACTTAAAGCTGCAGAGAG -3'
Posted On 2016-07-06