Incidental Mutation 'R7066:Sema5b'
ID 548594
Institutional Source Beutler Lab
Gene Symbol Sema5b
Ensembl Gene ENSMUSG00000052133
Gene Name sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B
Synonyms SemG, SemG, Semag
MMRRC Submission 045162-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7066 (G1)
Quality Score 220.009
Status Validated
Chromosome 16
Chromosomal Location 35361517-35485103 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 35471682 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Alanine at position 425 (D425A)
Ref Sequence ENSEMBL: ENSMUSP00000057494 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050625] [ENSMUST00000120756]
AlphaFold Q60519
Predicted Effect probably benign
Transcript: ENSMUST00000050625
AA Change: D425A

PolyPhen 2 Score 0.258 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: D425A

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Sema 68 479 1.68e-174 SMART
PSI 497 544 9.18e-12 SMART
TSP1 609 662 3.34e-15 SMART
TSP1 667 713 3.42e-12 SMART
TSP1 798 850 1.58e-16 SMART
TSP1 855 907 2.45e-13 SMART
TSP1 910 957 1.02e-1 SMART
transmembrane domain 977 999 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000120756
AA Change: D425A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: D425A

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Sema 68 479 1.68e-174 SMART
PSI 497 544 9.18e-12 SMART
TSP1 609 662 3.34e-15 SMART
TSP1 667 742 7.61e-10 SMART
TSP1 827 879 1.58e-16 SMART
TSP1 884 936 2.45e-13 SMART
TSP1 939 986 1.02e-1 SMART
transmembrane domain 1006 1028 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 98% (52/53)
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 protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a null mutation display defects in neurite arborization of multiple retinal cell types. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1cf T C 19: 31,904,514 (GRCm39) V175A probably damaging Het
Adamts5 A T 16: 85,659,652 (GRCm39) V880E probably damaging Het
Adgrf1 T A 17: 43,621,151 (GRCm39) F463I probably benign Het
Ano1 T A 7: 144,190,823 (GRCm39) E249D probably benign Het
Aoc1 A G 6: 48,885,553 (GRCm39) D686G probably damaging Het
Cacna1d A T 14: 30,074,935 (GRCm39) probably benign Het
Cdc42ep4 A G 11: 113,620,044 (GRCm39) S116P probably damaging Het
Ces2a T C 8: 105,466,880 (GRCm39) V463A probably damaging Het
Depdc5 A G 5: 33,059,192 (GRCm39) D297G probably benign Het
Fsip2 T A 2: 82,821,235 (GRCm39) V5656E possibly damaging Het
Gbp5 A G 3: 142,213,490 (GRCm39) T469A probably benign Het
Gm21663 C G 5: 26,146,259 (GRCm39) probably null Het
Iqch A G 9: 63,432,027 (GRCm39) V456A probably benign Het
Lpcat1 A C 13: 73,659,500 (GRCm39) I373L probably benign Het
Morc2b C T 17: 33,355,610 (GRCm39) V721I probably benign Het
Mrgprb1 C T 7: 48,097,424 (GRCm39) V163M probably benign Het
Mtfr2 A G 10: 20,229,972 (GRCm39) I142V possibly damaging Het
Muc16 A T 9: 18,569,317 (GRCm39) S1067R unknown Het
Myh14 T C 7: 44,280,179 (GRCm39) S892G possibly damaging Het
Mylk2 C T 2: 152,753,588 (GRCm39) probably null Het
Mzf1 A T 7: 12,777,490 (GRCm39) V638E possibly damaging Het
Ncoa1 C T 12: 4,372,934 (GRCm39) V156I possibly damaging Het
Nf1 A G 11: 79,447,546 (GRCm39) E2450G probably damaging Het
Or14j3 T A 17: 37,901,034 (GRCm39) D70V probably damaging Het
Or1e29 A G 11: 73,668,018 (GRCm39) I45T probably damaging Het
Or4a72 T C 2: 89,406,047 (GRCm39) T8A probably damaging Het
Or4f60 G A 2: 111,902,541 (GRCm39) P129L probably damaging Het
Or5t7 T A 2: 86,507,570 (GRCm39) T36S possibly damaging Het
Or6c88 T C 10: 129,407,373 (GRCm39) L283S probably damaging Het
Or8g54 A G 9: 39,707,420 (GRCm39) I250V probably benign Het
Or8k17 T C 2: 86,067,002 (GRCm39) D52G probably damaging Het
P4htm T G 9: 108,474,162 (GRCm39) K125N probably damaging Het
Patj A G 4: 98,301,434 (GRCm39) T240A probably benign Het
Pcolce2 T C 9: 95,563,674 (GRCm39) V220A probably benign Het
Pcyox1 A T 6: 86,371,478 (GRCm39) I136N probably damaging Het
Pde4b A G 4: 102,460,003 (GRCm39) S395G probably benign Het
Peg3 C A 7: 6,711,856 (GRCm39) R1122L probably damaging Het
Plekhm1 A G 11: 103,261,814 (GRCm39) V922A possibly damaging Het
Rad51c T C 11: 87,293,502 (GRCm39) N118S possibly damaging Het
Rb1cc1 T A 1: 6,320,229 (GRCm39) V1216D possibly damaging Het
Rictor C T 15: 6,801,635 (GRCm39) S441L probably benign Het
Rlf T C 4: 121,005,984 (GRCm39) M999V probably benign Het
Rsf1 GGCGGCGGC GGCGGCGGCCGCGGCGGC 7: 97,229,125 (GRCm39) probably benign Het
Samd7 G C 3: 30,805,272 (GRCm39) K18N probably benign Het
Siglecg A G 7: 43,061,166 (GRCm39) E413G probably benign Het
Tcaf1 A T 6: 42,656,111 (GRCm39) N288K probably damaging Het
Tdp1 A G 12: 99,860,991 (GRCm39) D210G probably benign Het
Umps A T 16: 33,782,103 (GRCm39) L273* probably null Het
Vcan A T 13: 89,853,805 (GRCm39) V385D probably damaging Het
Wdr59 T C 8: 112,192,477 (GRCm39) T676A probably benign Het
Zdbf2 A G 1: 63,346,718 (GRCm39) H1699R probably benign Het
Zfp27 AATCCGCTTGTGCA AA 7: 29,594,446 (GRCm39) probably benign Het
Other mutations in Sema5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00901:Sema5b APN 16 35,471,685 (GRCm39) missense probably damaging 1.00
IGL01584:Sema5b APN 16 35,465,793 (GRCm39) missense probably damaging 1.00
IGL01859:Sema5b APN 16 35,467,479 (GRCm39) missense possibly damaging 0.94
IGL02195:Sema5b APN 16 35,480,849 (GRCm39) critical splice acceptor site probably null
IGL02346:Sema5b APN 16 35,470,125 (GRCm39) missense probably damaging 1.00
IGL02850:Sema5b APN 16 35,480,885 (GRCm39) missense probably benign 0.01
IGL03277:Sema5b APN 16 35,471,682 (GRCm39) missense probably damaging 0.96
R0101:Sema5b UTSW 16 35,483,472 (GRCm39) splice site probably benign
R0368:Sema5b UTSW 16 35,448,470 (GRCm39) missense probably damaging 1.00
R0426:Sema5b UTSW 16 35,466,725 (GRCm39) missense probably damaging 1.00
R0675:Sema5b UTSW 16 35,480,703 (GRCm39) missense probably benign 0.00
R0905:Sema5b UTSW 16 35,443,001 (GRCm39) missense probably benign 0.33
R1163:Sema5b UTSW 16 35,448,466 (GRCm39) missense probably benign 0.19
R1195:Sema5b UTSW 16 35,472,030 (GRCm39) missense probably null 0.94
R1195:Sema5b UTSW 16 35,472,030 (GRCm39) missense probably null 0.94
R1666:Sema5b UTSW 16 35,478,852 (GRCm39) missense probably benign 0.03
R1706:Sema5b UTSW 16 35,470,125 (GRCm39) missense probably damaging 0.98
R1733:Sema5b UTSW 16 35,466,737 (GRCm39) missense probably damaging 1.00
R1775:Sema5b UTSW 16 35,480,694 (GRCm39) missense probably benign
R2215:Sema5b UTSW 16 35,480,585 (GRCm39) missense probably damaging 1.00
R2844:Sema5b UTSW 16 35,480,301 (GRCm39) missense probably damaging 0.98
R3086:Sema5b UTSW 16 35,443,093 (GRCm39) missense probably benign
R3613:Sema5b UTSW 16 35,480,520 (GRCm39) missense probably benign
R4774:Sema5b UTSW 16 35,483,552 (GRCm39) missense probably damaging 1.00
R5743:Sema5b UTSW 16 35,478,846 (GRCm39) missense probably damaging 1.00
R5856:Sema5b UTSW 16 35,466,756 (GRCm39) nonsense probably null
R5993:Sema5b UTSW 16 35,466,572 (GRCm39) missense probably damaging 1.00
R6248:Sema5b UTSW 16 35,448,377 (GRCm39) splice site probably null
R6420:Sema5b UTSW 16 35,483,516 (GRCm39) missense probably benign 0.08
R6795:Sema5b UTSW 16 35,478,941 (GRCm39) nonsense probably null
R6825:Sema5b UTSW 16 35,448,377 (GRCm39) splice site probably null
R7244:Sema5b UTSW 16 35,480,915 (GRCm39) missense probably benign
R7446:Sema5b UTSW 16 35,467,573 (GRCm39) missense probably damaging 1.00
R7497:Sema5b UTSW 16 35,481,700 (GRCm39) missense probably damaging 1.00
R7516:Sema5b UTSW 16 35,471,540 (GRCm39) missense probably benign 0.05
R7878:Sema5b UTSW 16 35,481,996 (GRCm39) missense probably benign 0.00
R7922:Sema5b UTSW 16 35,478,626 (GRCm39) frame shift probably null
R8397:Sema5b UTSW 16 35,471,691 (GRCm39) missense possibly damaging 0.59
R8537:Sema5b UTSW 16 35,471,979 (GRCm39) missense possibly damaging 0.49
R8929:Sema5b UTSW 16 35,467,737 (GRCm39) intron probably benign
R9262:Sema5b UTSW 16 35,453,223 (GRCm39) missense possibly damaging 0.57
R9389:Sema5b UTSW 16 35,466,092 (GRCm39) missense probably damaging 1.00
R9579:Sema5b UTSW 16 35,467,582 (GRCm39) missense probably benign 0.01
R9623:Sema5b UTSW 16 35,443,121 (GRCm39) missense possibly damaging 0.74
Z1088:Sema5b UTSW 16 35,480,960 (GRCm39) missense probably damaging 0.99
Z1176:Sema5b UTSW 16 35,470,234 (GRCm39) missense probably benign 0.01
Z1176:Sema5b UTSW 16 35,466,643 (GRCm39) missense probably benign 0.05
Z1176:Sema5b UTSW 16 35,448,388 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- CCATGAGAGTTCCCACTGTG -3'
(R):5'- CTTTCAGGATGGTACCCGACTC -3'

Sequencing Primer
(F):5'- GCACCAGTGACTCGGTTTC -3'
(R):5'- AGCCATGGCTTCTTACAG -3'
Posted On 2019-05-13