Incidental Mutation 'R9574:Sema3f'
ID 722208
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
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9574 (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 A at 107566972 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 186 (I186F)
Ref Sequence ENSEMBL: ENSMUSP00000141865 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000080560] [ENSMUST00000192727] [ENSMUST00000192783] [ENSMUST00000193108] [ENSMUST00000194039]
AlphaFold O88632
Predicted Effect possibly damaging
Transcript: ENSMUST00000080560
AA Change: I155F

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: I155F

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000192727
AA Change: I186F

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: I186F

DomainStartEndE-ValueType
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 silent
Transcript: ENSMUST00000192783
SMART Domains Protein: ENSMUSP00000141668
Gene: ENSMUSG00000034684

DomainStartEndE-ValueType
Sema 1 276 3.6e-7 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000193108
AA Change: I155F

PolyPhen 2 Score 0.613 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000141878
Gene: ENSMUSG00000034684
AA Change: I155F

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Sema 57 191 9.9e-46 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000194039
AA Change: I155F

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000142221
Gene: ENSMUSG00000034684
AA Change: I155F

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Sema 57 185 2e-42 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000194424
Predicted Effect
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930111J21Rik1 T A 11: 48,838,496 (GRCm39) E697V probably damaging Het
Actn4 T C 7: 28,594,864 (GRCm39) D805G probably benign Het
Adam2 C T 14: 66,275,071 (GRCm39) S554N probably benign Het
Adra2b A G 2: 127,206,283 (GRCm39) T267A probably benign Het
Apobec4 A T 1: 152,632,415 (GRCm39) T148S probably damaging Het
B4galt1 T A 4: 40,853,766 (GRCm39) M14L probably benign Het
Bok C A 1: 93,616,947 (GRCm39) Q98K probably benign Het
Cacnb4 A T 2: 52,327,016 (GRCm39) L394Q probably damaging Het
Ccar2 T C 14: 70,381,105 (GRCm39) K287E probably benign Het
Cdyl2 T A 8: 117,350,669 (GRCm39) E154V probably benign Het
Cenpn T G 8: 117,660,149 (GRCm39) Y160D probably damaging Het
Cfap20 T C 8: 96,149,514 (GRCm39) Y58C probably benign Het
Creb5 T A 6: 53,658,039 (GRCm39) L123Q unknown Het
Cspg4 G A 9: 56,797,342 (GRCm39) V1269M probably damaging Het
Cyp2b19 G T 7: 26,466,353 (GRCm39) K385N probably null Het
Cyp2b19 A T 7: 26,466,352 (GRCm39) K385M probably damaging Het
Ercc2 C A 7: 19,124,060 (GRCm39) D422E probably benign Het
Fbxl12 A G 9: 20,550,109 (GRCm39) V129A possibly damaging Het
Fbxo11 T C 17: 88,321,951 (GRCm39) E84G Het
Fmn1 T C 2: 113,425,402 (GRCm39) L1192S probably damaging Het
Galk2 T C 2: 125,824,979 (GRCm39) F392L probably benign Het
Gas2l3 G A 10: 89,258,135 (GRCm39) H153Y probably damaging Het
Gcn1 A T 5: 115,713,341 (GRCm39) K101N possibly damaging Het
Gmfg C T 7: 28,145,359 (GRCm39) Q101* probably null Het
Gpr108 C T 17: 57,545,039 (GRCm39) C309Y probably damaging Het
H3c8 T C 13: 23,719,761 (GRCm39) L49P probably damaging Het
Hscb A T 5: 110,982,595 (GRCm39) I164N probably damaging Het
Kifc2 T C 15: 76,546,397 (GRCm39) W260R probably damaging Het
Lrp6 T A 6: 134,447,662 (GRCm39) D995V possibly damaging Het
Lrrc1 T A 9: 77,358,708 (GRCm39) I308F probably damaging Het
Map7 C T 10: 20,153,966 (GRCm39) A694V unknown Het
Mapre2 A G 18: 23,965,993 (GRCm39) D68G probably benign Het
Mertk A T 2: 128,593,880 (GRCm39) I295F probably benign Het
Mst1 T A 9: 107,962,053 (GRCm39) C690* probably null Het
Nde1 A G 16: 13,988,345 (GRCm39) E76G probably damaging Het
Nek5 T C 8: 22,564,040 (GRCm39) T597A probably benign Het
Nup210l T C 3: 90,117,693 (GRCm39) F1800L probably benign Het
Or5c1 A G 2: 37,222,148 (GRCm39) I130V possibly damaging Het
Pdpn T A 4: 142,997,101 (GRCm39) D131V probably benign Het
Pgap6 T C 17: 26,337,861 (GRCm39) V415A probably damaging Het
Pot1a T C 6: 25,775,718 (GRCm39) T118A possibly damaging Het
Prom1 A G 5: 44,158,179 (GRCm39) I843T probably benign Het
Prrt3 T C 6: 113,474,587 (GRCm39) T212A probably benign Het
Rabgap1 A G 2: 37,433,246 (GRCm39) probably null Het
Rarb A T 14: 16,574,858 (GRCm38) S53T probably damaging Het
Rnft2 A G 5: 118,375,330 (GRCm39) S140P probably benign Het
Rxfp1 T C 3: 79,563,581 (GRCm39) M362V probably benign Het
Sall2 G A 14: 52,551,617 (GRCm39) T526M probably damaging Het
Scube1 T C 15: 83,501,000 (GRCm39) D598G Het
Shank2 A G 7: 143,622,462 (GRCm39) T199A possibly damaging Het
Sipa1l2 T A 8: 126,169,453 (GRCm39) M1427L probably benign Het
Sis C T 3: 72,828,490 (GRCm39) G1195D probably benign Het
Slc25a39 A T 11: 102,295,390 (GRCm39) H193Q probably benign Het
Sprr2b CTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCC CTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCC 3: 92,224,826 (GRCm39) probably benign Het
Srgn A C 10: 62,343,444 (GRCm39) L17R probably damaging Het
Stard5 A G 7: 83,281,944 (GRCm39) N34D probably benign Het
Syt8 A T 7: 141,993,203 (GRCm39) D220V probably damaging Het
Tex15 A G 8: 34,064,509 (GRCm39) E1313G probably benign Het
Tmem131l T C 3: 83,868,911 (GRCm39) R155G probably damaging Het
Tmem220 T C 11: 66,916,093 (GRCm39) V30A probably damaging Het
Tollip A G 7: 141,445,731 (GRCm39) I119T probably damaging Het
Treml4 G A 17: 48,571,672 (GRCm39) G25D probably damaging Het
Trim7 T C 11: 48,728,460 (GRCm39) F36S probably damaging Het
Txnrd3 T A 6: 89,640,166 (GRCm39) C293* probably null Het
Utp14b A G 1: 78,643,482 (GRCm39) D460G probably benign Het
Vmn2r41 T A 7: 8,153,329 (GRCm39) N397Y probably benign Het
Vmn2r67 T C 7: 84,786,017 (GRCm39) I663V probably benign Het
Zfp292 T A 4: 34,839,460 (GRCm39) H135L probably damaging Het
Zfp420 C T 7: 29,575,480 (GRCm39) R567* probably null Het
Zfp518b C T 5: 38,830,773 (GRCm39) V411M probably benign Het
Zfp638 T A 6: 83,956,680 (GRCm39) D1762E probably damaging Het
Zfp691 T A 4: 119,028,230 (GRCm39) M1L 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
R7449:Sema3f UTSW 9 107,561,235 (GRCm39) missense probably damaging 1.00
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
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
(F):5'- AACCCTCTCTAGGCAAGTCC -3'
(R):5'- AATACCATGGGCTTGCCCTAG -3'

Sequencing Primer
(F):5'- TCTAGGCAAGTCCCCACTG -3'
(R):5'- ATGGGCTTGCCCTAGGAGAC -3'
Posted On 2022-08-09