Incidental Mutation 'R1195:Sema5b'
ID 101081
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 039267-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1195 (G1)
Quality Score 126
Status Not validated
Chromosome 16
Chromosomal Location 35361517-35485103 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 35472030 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Valine at position 496 (E496V)
Ref Sequence ENSEMBL: ENSMUSP00000112536 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000050625] [ENSMUST00000120756]
AlphaFold Q60519
Predicted Effect probably null
Transcript: ENSMUST00000050625
AA Change: E496V

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: E496V

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 null
Transcript: ENSMUST00000120756
AA Change: E496V

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: E496V

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133554
Meta Mutation Damage Score 0.1953 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.5%
  • 10x: 93.1%
  • 20x: 81.3%
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 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: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agtr1a C A 13: 30,565,901 (GRCm39) P322Q probably damaging Het
Amh AGCGCCTTGG AG 10: 80,641,419 (GRCm39) probably null Het
Brd1 T C 15: 88,585,014 (GRCm39) E940G probably benign Het
Cd28 C T 1: 60,802,303 (GRCm39) T74I possibly damaging Het
Cntnap2 T A 6: 46,460,902 (GRCm39) M646K probably benign Het
Cyb5d1 C T 11: 69,285,797 (GRCm39) probably null Het
D6Ertd527e C G 6: 87,088,506 (GRCm39) T223S unknown Het
Dst A G 1: 34,250,235 (GRCm39) D4063G probably damaging Het
Elmod1 T C 9: 53,843,052 (GRCm39) Y42C probably damaging Het
Hdac5 T C 11: 102,096,332 (GRCm39) I310V probably damaging Het
Ighv10-1 A T 12: 114,443,015 (GRCm39) probably benign Het
Igsf3 A G 3: 101,365,419 (GRCm39) D1130G probably benign Het
Katnip A G 7: 125,465,654 (GRCm39) R1343G probably damaging Het
Kdm4d A G 9: 14,374,395 (GRCm39) S488P probably benign Het
Lingo2 A G 4: 35,708,538 (GRCm39) Y481H probably damaging Het
Ltbp1 A G 17: 75,532,280 (GRCm39) Q118R possibly damaging Het
Map3k20 C T 2: 72,268,562 (GRCm39) P523L probably damaging Het
Msx1 A G 5: 37,978,625 (GRCm39) Y297H probably damaging Het
Myo9a A G 9: 59,802,483 (GRCm39) D1990G probably damaging Het
Niban2 T C 2: 32,809,815 (GRCm39) V304A probably benign Het
Perp C A 10: 18,731,483 (GRCm39) Y147* probably null Het
Prr16 A T 18: 51,435,755 (GRCm39) D78V probably damaging Het
Rfx7 C T 9: 72,525,228 (GRCm39) T806M probably damaging Het
Robo2 T C 16: 73,713,016 (GRCm39) probably null Het
Shf G A 2: 122,199,163 (GRCm39) P51S probably damaging Het
Spdl1 T C 11: 34,710,644 (GRCm39) Y368C probably damaging Het
Sptbn2 G C 19: 4,795,921 (GRCm39) R1700P possibly damaging Het
Tenm2 C T 11: 35,954,004 (GRCm39) G1236R possibly damaging Het
Tln2 T G 9: 67,165,848 (GRCm39) K1000Q probably damaging Het
Tmbim7 A G 5: 3,711,943 (GRCm39) T63A probably benign Het
Tmed11 T C 5: 108,926,885 (GRCm39) D129G possibly damaging Het
Ttc28 G A 5: 111,373,543 (GRCm39) S962N probably damaging Het
Ttll6 T C 11: 96,026,555 (GRCm39) I113T probably damaging Het
Uso1 T A 5: 92,318,606 (GRCm39) F210L probably damaging Het
Uspl1 T A 5: 149,131,131 (GRCm39) V224E probably benign Het
Zfp639 G A 3: 32,573,345 (GRCm39) V86I possibly damaging 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
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
R7066:Sema5b UTSW 16 35,471,682 (GRCm39) missense probably benign 0.26
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'- GCAAGCTAAGGACACGCTCTATCAC -3'
(R):5'- TAAATTCATGGCTCCCTCGGGCAG -3'

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