Incidental Mutation 'R7449:Sema3f'
ID 577571
Institutional Source Beutler Lab
Gene Symbol Sema3f
Ensembl Gene ENSMUSG00000034684
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F
Synonyms Sema IV, Semak
MMRRC Submission 045524-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7449 (G1)
Quality Score 225.009
Status Not validated
Chromosome 9
Chromosomal Location 107558699-107587674 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 107561235 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 584 (S584G)
Ref Sequence ENSEMBL: ENSMUSP00000141865 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000010205] [ENSMUST00000080560] [ENSMUST00000192271] [ENSMUST00000192727] [ENSMUST00000192783] [ENSMUST00000193108] [ENSMUST00000194039]
AlphaFold O88632
Predicted Effect probably benign
Transcript: ENSMUST00000010205
SMART Domains Protein: ENSMUSP00000010205
Gene: ENSMUSG00000034837

G_alpha 9 349 5.13e-223 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000080560
AA Change: S553G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: S553G

signal peptide 1 18 N/A INTRINSIC
Sema 57 498 5.46e-206 SMART
PSI 516 568 1.87e-12 SMART
IGc2 586 654 3.79e-4 SMART
low complexity region 673 695 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192271
SMART Domains Protein: ENSMUSP00000141571
Gene: ENSMUSG00000034837

low complexity region 14 27 N/A INTRINSIC
transmembrane domain 32 49 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000192727
AA Change: S584G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: S584G

signal peptide 1 18 N/A INTRINSIC
Sema 57 529 3.31e-205 SMART
PSI 547 599 1.87e-12 SMART
IGc2 617 685 3.79e-4 SMART
low complexity region 704 726 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192783
SMART Domains Protein: ENSMUSP00000141668
Gene: ENSMUSG00000034684

Sema 1 276 3.6e-7 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000193108
SMART Domains Protein: ENSMUSP00000141878
Gene: ENSMUSG00000034684

signal peptide 1 18 N/A INTRINSIC
Pfam:Sema 57 191 9.9e-46 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000194039
SMART Domains Protein: ENSMUSP00000142221
Gene: ENSMUSG00000034684

signal peptide 1 18 N/A INTRINSIC
Pfam:Sema 57 185 2e-42 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000194424
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
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 loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
PHENOTYPE: Inactivation of this locus results in neuronal defects including impaired CNS axon pathfinding, and PNS and limbic system circuitry. Mice homozygous for a knock-out allele exhibit increased lymphatic branching complexity and LEC numbers. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 T A 7: 120,035,131 (GRCm39) Y306N possibly damaging Het
Adgrv1 A T 13: 81,647,192 (GRCm39) V3116D probably damaging Het
Adss1 A T 12: 112,600,585 (GRCm39) T185S probably damaging Het
Ago2 G A 15: 73,018,348 (GRCm39) P30L probably damaging Het
Arb2a A G 13: 77,907,561 (GRCm39) I41V probably damaging Het
Atp5pf C T 16: 84,628,251 (GRCm39) V44M probably benign Het
Atp7b T A 8: 22,501,865 (GRCm39) I833F probably damaging Het
Birc6 T A 17: 75,009,336 (GRCm39) N4869K probably benign Het
Cacna1c C T 6: 118,579,310 (GRCm39) D1796N Het
Ccng2 C G 5: 93,421,202 (GRCm39) S237R probably benign Het
Cnga1 A G 5: 72,762,647 (GRCm39) I289T probably benign Het
Crybg1 C A 10: 43,880,515 (GRCm39) E224D probably benign Het
Dysf T C 6: 84,114,362 (GRCm39) L1217P possibly damaging Het
Ebf2 T A 14: 67,647,469 (GRCm39) N339K probably damaging Het
Eva1c T C 16: 90,673,081 (GRCm39) probably null Het
Fam184a T C 10: 53,574,730 (GRCm39) E293G probably damaging Het
Folh1 G A 7: 86,380,956 (GRCm39) P506S probably benign Het
Ftcd A T 10: 76,415,997 (GRCm39) K210N probably benign Het
Gdf6 T A 4: 9,844,494 (GRCm39) V6D possibly damaging Het
Ghitm C A 14: 36,853,538 (GRCm39) G101C probably damaging Het
Gimap5 T A 6: 48,729,838 (GRCm39) V136D probably damaging Het
Grm4 C T 17: 27,654,345 (GRCm39) G535D probably damaging Het
Gse1 T C 8: 120,956,450 (GRCm39) S314P unknown Het
Hnrnpdl A G 5: 100,185,014 (GRCm39) I279T probably damaging Het
Idi2l T A 13: 8,993,340 (GRCm39) H51L probably damaging Het
Itpr1 T C 6: 108,366,345 (GRCm39) S923P probably damaging Het
Krt39 C A 11: 99,408,887 (GRCm39) C303F probably benign Het
Lrrn1 T C 6: 107,545,482 (GRCm39) S427P possibly damaging Het
Lrrn3 T A 12: 41,503,487 (GRCm39) R277W probably damaging Het
Ltb4r1 T C 14: 56,005,375 (GRCm39) L226P probably damaging Het
Map1b C T 13: 99,644,648 (GRCm39) R85Q probably damaging Het
Mcoln1 T C 8: 3,557,285 (GRCm39) L125P probably damaging Het
Nid1 T G 13: 13,656,636 (GRCm39) V589G probably damaging Het
Nlrp5 T G 7: 23,116,951 (GRCm39) F225C probably benign Het
Notch3 C T 17: 32,376,940 (GRCm39) A322T probably damaging Het
Or14c43 A G 7: 86,115,063 (GRCm39) H148R probably benign Het
Or52a5b G T 7: 103,417,026 (GRCm39) Q193K probably benign Het
Or7g34 T A 9: 19,478,162 (GRCm39) T173S probably benign Het
Otogl A G 10: 107,639,524 (GRCm39) C1363R probably damaging Het
Ovol1 T A 19: 5,603,625 (GRCm39) D92V probably benign Het
Pigt T C 2: 164,344,419 (GRCm39) L356P probably damaging Het
Plekhg3 A G 12: 76,612,996 (GRCm39) Q434R probably damaging Het
Plekhh1 T C 12: 79,126,326 (GRCm39) F1344L probably benign Het
Polr1has A G 17: 37,275,275 (GRCm39) D16G probably damaging Het
Psmd3 T A 11: 98,586,377 (GRCm39) L515Q probably damaging Het
Pus1 A G 5: 110,922,452 (GRCm39) L405P probably damaging Het
Qtrt2 T A 16: 43,701,395 (GRCm39) H55L probably benign Het
Rasgrp1 T C 2: 117,118,424 (GRCm39) I522V probably damaging Het
Raver2 T A 4: 100,959,860 (GRCm39) H113Q probably damaging Het
Recql4 T C 15: 76,589,765 (GRCm39) D760G unknown Het
Rhobtb3 C T 13: 76,058,860 (GRCm39) V313M probably benign Het
Rhox4d G A X: 36,700,645 (GRCm39) G191E unknown Het
Rictor C T 15: 6,801,635 (GRCm39) S441L probably benign Het
Rnf185 T C 11: 3,376,578 (GRCm39) Q135R probably benign Het
Sh3pxd2a T A 19: 47,256,091 (GRCm39) T904S probably benign Het
Slc4a10 T C 2: 62,134,290 (GRCm39) V1002A probably benign Het
Taf1b T C 12: 24,554,992 (GRCm39) I55T probably benign Het
Tenm4 A T 7: 96,523,420 (GRCm39) D1654V possibly damaging Het
Tgfb1 G A 7: 25,404,263 (GRCm39) V357M probably damaging Het
Tnxb C T 17: 34,922,335 (GRCm39) P2383S possibly damaging Het
Trpm1 A T 7: 63,858,723 (GRCm39) M382L probably benign Het
Trrap A G 5: 144,788,019 (GRCm39) Y3516C probably damaging Het
Txnrd1 T A 10: 82,721,067 (GRCm39) Y494* probably null Het
Ubr2 C T 17: 47,275,714 (GRCm39) E811K probably damaging Het
Ubxn4 T A 1: 128,172,280 (GRCm39) F25I possibly damaging Het
Vmn2r117 A G 17: 23,678,869 (GRCm39) M785T probably damaging Het
Vmn2r99 G A 17: 19,599,407 (GRCm39) D364N probably benign Het
Vps45 C A 3: 95,954,448 (GRCm39) probably null Het
Wdr25 A C 12: 108,992,367 (GRCm39) H426P probably damaging Het
Wdr83 A T 8: 85,806,310 (GRCm39) W136R probably damaging Het
Xylt1 A C 7: 117,191,232 (GRCm39) I343L possibly damaging Het
Zscan4b T C 7: 10,637,985 (GRCm39) Q53R possibly damaging Het
Other mutations in Sema3f
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00945:Sema3f APN 9 107,562,721 (GRCm39) missense probably benign 0.44
IGL01940:Sema3f APN 9 107,560,896 (GRCm39) unclassified probably benign
IGL02070:Sema3f APN 9 107,569,440 (GRCm39) missense probably damaging 1.00
IGL02381:Sema3f APN 9 107,569,594 (GRCm39) missense probably damaging 1.00
IGL02472:Sema3f APN 9 107,564,935 (GRCm39) missense probably damaging 1.00
IGL02557:Sema3f APN 9 107,564,411 (GRCm39) missense probably damaging 1.00
IGL02614:Sema3f APN 9 107,559,710 (GRCm39) missense probably benign 0.28
IGL02660:Sema3f APN 9 107,561,183 (GRCm39) missense probably benign 0.05
R1468:Sema3f UTSW 9 107,564,771 (GRCm39) unclassified probably benign
R1905:Sema3f UTSW 9 107,561,575 (GRCm39) missense probably damaging 1.00
R4728:Sema3f UTSW 9 107,582,639 (GRCm39) missense probably benign 0.00
R4772:Sema3f UTSW 9 107,566,919 (GRCm39) nonsense probably null
R4786:Sema3f UTSW 9 107,559,881 (GRCm39) missense probably benign 0.45
R4845:Sema3f UTSW 9 107,562,700 (GRCm39) missense probably damaging 1.00
R5418:Sema3f UTSW 9 107,569,820 (GRCm39) missense probably damaging 1.00
R5780:Sema3f UTSW 9 107,559,788 (GRCm39) missense probably damaging 0.98
R5849:Sema3f UTSW 9 107,559,815 (GRCm39) missense probably damaging 0.98
R5929:Sema3f UTSW 9 107,569,392 (GRCm39) missense probably damaging 1.00
R6968:Sema3f UTSW 9 107,568,648 (GRCm39) critical splice acceptor site probably null
R7043:Sema3f UTSW 9 107,568,599 (GRCm39) missense possibly damaging 0.91
R7526:Sema3f UTSW 9 107,566,927 (GRCm39) missense probably damaging 0.96
R7559:Sema3f UTSW 9 107,561,777 (GRCm39) missense possibly damaging 0.52
R7640:Sema3f UTSW 9 107,560,774 (GRCm39) missense probably benign 0.20
R7771:Sema3f UTSW 9 107,569,625 (GRCm39) missense possibly damaging 0.89
R7789:Sema3f UTSW 9 107,582,631 (GRCm39) missense probably benign 0.00
R8058:Sema3f UTSW 9 107,559,800 (GRCm39) missense probably benign 0.42
R8113:Sema3f UTSW 9 107,565,275 (GRCm39) missense possibly damaging 0.95
R9574:Sema3f UTSW 9 107,566,972 (GRCm39) missense possibly damaging 0.50
R9641:Sema3f UTSW 9 107,565,454 (GRCm39) missense unknown
R9674:Sema3f UTSW 9 107,566,947 (GRCm39) missense possibly damaging 0.69
R9799:Sema3f UTSW 9 107,562,562 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2019-10-07