Incidental Mutation 'R1184:Sema4b'
ID 101915
Institutional Source Beutler Lab
Gene Symbol Sema4b
Ensembl Gene ENSMUSG00000030539
Gene Name sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B
Synonyms SemC, Semac
MMRRC Submission 039256-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.771) question?
Stock # R1184 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 79836589-79876275 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 79874388 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 593 (T593A)
Ref Sequence ENSEMBL: ENSMUSP00000145622 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032754] [ENSMUST00000065163] [ENSMUST00000071457] [ENSMUST00000123279] [ENSMUST00000205822] [ENSMUST00000205996] [ENSMUST00000206802] [ENSMUST00000206084]
AlphaFold Q62179
Predicted Effect probably benign
Transcript: ENSMUST00000032754
AA Change: T593A

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000032754
Gene: ENSMUSG00000030539
AA Change: T593A

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
Sema 57 494 8.07e-177 SMART
PSI 512 582 4.7e-9 SMART
low complexity region 626 639 N/A INTRINSIC
transmembrane domain 701 723 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000065163
SMART Domains Protein: ENSMUSP00000070901
Gene: ENSMUSG00000030538

DomainStartEndE-ValueType
low complexity region 84 100 N/A INTRINSIC
EFh 107 135 4.4e0 SMART
EFh 152 180 1.17e-2 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000071457
SMART Domains Protein: ENSMUSP00000071401
Gene: ENSMUSG00000030538

DomainStartEndE-ValueType
low complexity region 36 52 N/A INTRINSIC
EFh 59 87 4.4e0 SMART
EFh 104 132 1.17e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000107383
SMART Domains Protein: ENSMUSP00000103006
Gene: ENSMUSG00000030539

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
Sema 57 494 8.07e-177 SMART
PSI 512 550 2.68e-4 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000123279
SMART Domains Protein: ENSMUSP00000118926
Gene: ENSMUSG00000030538

DomainStartEndE-ValueType
low complexity region 10 26 N/A INTRINSIC
EFh 33 61 4.4e0 SMART
EFh 78 106 1.17e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131402
Predicted Effect probably benign
Transcript: ENSMUST00000205822
AA Change: T593A

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)
Predicted Effect probably benign
Transcript: ENSMUST00000205996
Predicted Effect probably benign
Transcript: ENSMUST00000206802
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206211
Predicted Effect probably benign
Transcript: ENSMUST00000206084
Meta Mutation Damage Score 0.0693 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.5%
Validation Efficiency 100% (83/83)
MGI Phenotype PHENOTYPE: Mice homozygous for a gene trap allele exhibit normal cerebellar morphology. Mice homozygous for a knock-out allele exhibit enhanced memory response by way of increased IgE and IgG1 serum levels. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700003E16Rik A G 6: 83,137,894 (GRCm39) R7G probably damaging Het
Ahdc1 T A 4: 132,792,707 (GRCm39) M1316K probably benign Het
Alkal1 A G 1: 6,459,712 (GRCm39) Y96C probably damaging Het
Anxa2r1 A T 13: 120,496,667 (GRCm39) N67K probably benign Het
Arhgap17 T C 7: 122,913,913 (GRCm39) Y199C probably damaging Het
Bmp2 T C 2: 133,403,388 (GRCm39) V313A probably damaging Het
Cacna1b C T 2: 24,577,757 (GRCm39) probably null Het
Cars1 T C 7: 143,140,876 (GRCm39) T141A probably damaging Het
Ccdc57 A G 11: 120,764,637 (GRCm39) probably benign Het
Cenpe T C 3: 134,970,183 (GRCm39) probably null Het
Chadl T C 15: 81,577,258 (GRCm39) S198G probably benign Het
Chd6 G C 2: 160,872,722 (GRCm39) P286R probably damaging Het
Clec4a4 G T 6: 122,989,671 (GRCm39) W104L probably benign Het
Coq4 G A 2: 29,678,346 (GRCm39) probably benign Het
Cplane1 G T 15: 8,245,971 (GRCm39) V1448L probably benign Het
Crtc2 T A 3: 90,169,940 (GRCm39) Y445* probably null Het
Dapk1 A T 13: 60,844,112 (GRCm39) I44F probably damaging Het
Dcbld2 T A 16: 58,270,204 (GRCm39) probably null Het
Dcun1d4 T C 5: 73,668,455 (GRCm39) probably benign Het
Depdc7 A T 2: 104,560,523 (GRCm39) probably benign Het
Dna2 A G 10: 62,794,977 (GRCm39) D416G probably benign Het
Dnah2 A T 11: 69,390,016 (GRCm39) I743N probably damaging Het
Dnah9 A G 11: 65,975,438 (GRCm39) probably null Het
Dock3 A G 9: 106,846,999 (GRCm39) S877P probably damaging Het
Eif3l T A 15: 78,959,966 (GRCm39) probably null Het
Epha5 A T 5: 84,219,134 (GRCm39) probably null Het
Ffar3 T A 7: 30,554,529 (GRCm39) N264Y probably damaging Het
Fyb1 A T 15: 6,668,381 (GRCm39) I525F probably damaging Het
Fyco1 A G 9: 123,648,218 (GRCm39) F1239L probably damaging Het
Gcdh T C 8: 85,620,071 (GRCm39) probably benign Het
Gk5 T C 9: 96,032,473 (GRCm39) probably benign Het
Grm1 A G 10: 10,595,778 (GRCm39) Y617H probably benign Het
Gvin-ps3 A G 7: 105,683,159 (GRCm39) V32A probably benign Het
Hhipl2 A T 1: 183,206,042 (GRCm39) I131L probably damaging Het
Larp4b T C 13: 9,216,345 (GRCm39) probably benign Het
Lrig2 T A 3: 104,398,227 (GRCm39) I301F possibly damaging Het
Man2a2 A T 7: 80,012,713 (GRCm39) I600N possibly damaging Het
Mylk2 G C 2: 152,755,661 (GRCm39) probably null Het
Myo6 C T 9: 80,193,664 (GRCm39) Q870* probably null Het
Napg T G 18: 63,127,409 (GRCm39) H204Q probably benign Het
Neb G A 2: 52,153,959 (GRCm39) T2384M probably damaging Het
Nek10 A G 14: 14,931,325 (GRCm38) probably benign Het
Or11h23 A C 14: 50,948,071 (GRCm39) T95P probably benign Het
Or4c111 A G 2: 88,844,057 (GRCm39) M117T probably damaging Het
Or5an6 T C 19: 12,372,221 (GRCm39) V198A probably benign Het
Or5b108 T G 19: 13,168,739 (GRCm39) L236R probably damaging Het
Pclo A G 5: 14,572,276 (GRCm39) T554A unknown Het
Perm1 C A 4: 156,301,771 (GRCm39) T105K probably damaging Het
Pik3r1 T C 13: 101,822,866 (GRCm39) probably null Het
Pld5 A G 1: 175,872,462 (GRCm39) I225T probably damaging Het
Plxnc1 T C 10: 94,667,195 (GRCm39) probably benign Het
Ptpn12 A C 5: 21,203,354 (GRCm39) S475A possibly damaging Het
Ptprt A G 2: 161,769,692 (GRCm39) V391A possibly damaging Het
Rac2 T G 15: 78,450,145 (GRCm39) D65A possibly damaging Het
Rgl3 A G 9: 21,888,676 (GRCm39) probably null Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Sebox A T 11: 78,394,675 (GRCm39) T47S probably damaging Het
Serpina3a C T 12: 104,082,787 (GRCm39) Q187* probably null Het
Serpinb1a T C 13: 33,027,199 (GRCm39) K248E probably benign Het
Serpinb9e A C 13: 33,443,757 (GRCm39) E259A probably benign Het
Slc30a3 T A 5: 31,247,510 (GRCm39) H44L probably damaging Het
Smarca2 T C 19: 26,748,333 (GRCm39) probably benign Het
Snrnp200 T A 2: 127,078,737 (GRCm39) C1801S probably damaging Het
Soat1 G A 1: 156,269,944 (GRCm39) probably null Het
Spink6 T C 18: 44,204,605 (GRCm39) probably benign Het
Spta1 G A 1: 174,012,256 (GRCm39) R354H probably damaging Het
Tbck T A 3: 132,543,733 (GRCm39) H861Q probably benign Het
Tgfbrap1 G A 1: 43,088,856 (GRCm39) T849M possibly damaging Het
Tnrc6a A G 7: 122,769,563 (GRCm39) N451S possibly damaging Het
Trim36 T C 18: 46,329,318 (GRCm39) T41A probably damaging Het
Trmt112 C A 19: 6,887,721 (GRCm39) probably benign Het
Trpc4ap A G 2: 155,486,990 (GRCm39) probably benign Het
Ttll7 C T 3: 146,645,746 (GRCm39) P535S probably damaging Het
Ttn A T 2: 76,691,776 (GRCm39) probably benign Het
Txndc11 C T 16: 10,946,364 (GRCm39) R149Q probably benign Het
Ubr4 C T 4: 139,164,509 (GRCm39) probably benign Het
Usp30 G A 5: 114,241,888 (GRCm39) probably null Het
Vmn1r195 A G 13: 22,463,181 (GRCm39) Y217C probably damaging Het
Vps33b T A 7: 79,932,234 (GRCm39) D135E probably benign Het
Vrk2 A G 11: 26,433,331 (GRCm39) probably benign Het
Wdr81 G T 11: 75,343,809 (GRCm39) P486Q probably damaging Het
Zfp788 T C 7: 41,297,750 (GRCm39) Y129H probably damaging Het
Other mutations in Sema4b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01538:Sema4b APN 7 79,865,444 (GRCm39) missense probably damaging 1.00
IGL02584:Sema4b APN 7 79,874,736 (GRCm39) missense probably benign
IGL02657:Sema4b APN 7 79,866,789 (GRCm39) missense probably damaging 1.00
false_flag UTSW 7 79,848,402 (GRCm39) start codon destroyed probably null
R0114:Sema4b UTSW 7 79,868,826 (GRCm39) splice site probably benign
R0480:Sema4b UTSW 7 79,869,954 (GRCm39) missense probably damaging 1.00
R1545:Sema4b UTSW 7 79,868,771 (GRCm39) missense probably benign 0.02
R1687:Sema4b UTSW 7 79,869,010 (GRCm39) missense probably damaging 1.00
R1880:Sema4b UTSW 7 79,866,540 (GRCm39) missense probably damaging 0.96
R1881:Sema4b UTSW 7 79,866,540 (GRCm39) missense probably damaging 0.96
R2180:Sema4b UTSW 7 79,862,583 (GRCm39) missense probably benign 0.28
R2352:Sema4b UTSW 7 79,870,627 (GRCm39) missense probably damaging 0.99
R2424:Sema4b UTSW 7 79,869,023 (GRCm39) missense probably damaging 1.00
R3913:Sema4b UTSW 7 79,870,222 (GRCm39) missense probably benign
R4353:Sema4b UTSW 7 79,865,399 (GRCm39) missense probably damaging 1.00
R4757:Sema4b UTSW 7 79,866,577 (GRCm39) missense probably damaging 1.00
R4921:Sema4b UTSW 7 79,848,504 (GRCm39) missense possibly damaging 0.77
R5004:Sema4b UTSW 7 79,866,093 (GRCm39) missense probably benign 0.13
R5399:Sema4b UTSW 7 79,874,634 (GRCm39) missense probably benign
R5599:Sema4b UTSW 7 79,863,039 (GRCm39) missense probably benign 0.40
R5820:Sema4b UTSW 7 79,874,706 (GRCm39) missense probably damaging 0.99
R5840:Sema4b UTSW 7 79,868,697 (GRCm39) missense probably damaging 1.00
R5901:Sema4b UTSW 7 79,874,715 (GRCm39) missense possibly damaging 0.49
R6600:Sema4b UTSW 7 79,862,676 (GRCm39) missense probably benign 0.42
R6749:Sema4b UTSW 7 79,869,949 (GRCm39) missense possibly damaging 0.56
R6992:Sema4b UTSW 7 79,869,900 (GRCm39) missense probably damaging 0.97
R7175:Sema4b UTSW 7 79,848,402 (GRCm39) start codon destroyed probably null
R7660:Sema4b UTSW 7 79,869,995 (GRCm39) missense probably benign 0.01
R8345:Sema4b UTSW 7 79,870,567 (GRCm39) missense probably damaging 0.98
R8819:Sema4b UTSW 7 79,870,248 (GRCm39) missense probably damaging 1.00
R8820:Sema4b UTSW 7 79,870,248 (GRCm39) missense probably damaging 1.00
R8960:Sema4b UTSW 7 79,875,076 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAGTCACTTAGTCCCAACCATCGC -3'
(R):5'- CCACAAGCTGCTGGAATCCTTCTTC -3'

Sequencing Primer
(F):5'- tcagtggacagcagggag -3'
(R):5'- TTCTTCTATCGACCAACACTGGAAC -3'
Posted On 2014-01-15