Incidental Mutation 'R0373:Sema3b'
ID 30626
Institutional Source Beutler Lab
Gene Symbol Sema3b
Ensembl Gene ENSMUSG00000057969
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B
Synonyms semaV, Semaa, SemA, sema5, SemA, LUCA-1
MMRRC Submission 038579-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.341) question?
Stock # R0373 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 107474873-107486428 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 107480117 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 207 (N207S)
Ref Sequence ENSEMBL: ENSMUSP00000099591 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073448] [ENSMUST00000102529] [ENSMUST00000102530] [ENSMUST00000102531] [ENSMUST00000102532] [ENSMUST00000123926] [ENSMUST00000193180] [ENSMUST00000194433] [ENSMUST00000195662] [ENSMUST00000194606] [ENSMUST00000195057]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000073448
AA Change: N207S

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
PSI 515 567 1.77e-13 SMART
IG 577 660 7.7e-5 SMART
low complexity region 665 683 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102529
AA Change: N207S

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
PSI 515 567 1.77e-13 SMART
IG 577 660 7.7e-5 SMART
low complexity region 665 683 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102530
AA Change: N207S

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
PSI 515 567 1.77e-13 SMART
IG 577 660 7.7e-5 SMART
low complexity region 665 683 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102531
AA Change: N207S

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
PSI 515 567 1.77e-13 SMART
IG 577 660 7.7e-5 SMART
low complexity region 665 683 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102532
AA Change: N207S

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
PSI 515 567 1.77e-13 SMART
IG 577 660 7.7e-5 SMART
low complexity region 665 683 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123926
AA Change: N207S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: N207S

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Sema 55 497 6.37e-207 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000193180
SMART Domains Protein: ENSMUSP00000141726
Gene: ENSMUSG00000057969

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:Sema 55 148 8.2e-31 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195472
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193234
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193551
Predicted Effect probably benign
Transcript: ENSMUST00000194433
SMART Domains Protein: ENSMUSP00000141403
Gene: ENSMUSG00000057969

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:Sema 55 172 3.5e-36 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000195662
SMART Domains Protein: ENSMUSP00000141614
Gene: ENSMUSG00000057969

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:Sema 55 137 8.4e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000194606
Predicted Effect probably benign
Transcript: ENSMUST00000195057
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.1%
  • 10x: 95.8%
  • 20x: 91.5%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a secreted protein that belongs to the class 3 semaphorin/collapsin family. Members of this family play a role in growth cone guidance during neurogenesis. The encoded protein inhibits axonal extension. This protein is thought to be an osteoblast protein that regulates bone mass and affects skeletal homeostasis. A similar gene in humans functions as a tumor suppressor gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for one knock-out allele are viable and fertile with no obvious pathological abnormalities. Mice homozygous for a second knock-out allele exhibit improper positioning of a major brain commissural projection, the anterior commissure. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579F01Rik A T 3: 137,879,343 (GRCm39) L235Q probably damaging Het
Aadacl4fm4 A T 4: 144,412,790 (GRCm39) M50K possibly damaging Het
Adam6b T A 12: 113,454,275 (GRCm39) V364D probably benign Het
Akap13 T C 7: 75,259,677 (GRCm39) L767P probably benign Het
Akap13 T A 7: 75,380,248 (GRCm39) S2193T probably damaging Het
Anapc11 T C 11: 120,496,203 (GRCm39) V69A probably benign Het
Ankmy1 C T 1: 92,823,912 (GRCm39) R118Q probably damaging Het
Ankrd27 T C 7: 35,337,478 (GRCm39) S931P probably benign Het
Atp6v1c2 G A 12: 17,338,169 (GRCm39) R280C probably damaging Het
Bbs10 T A 10: 111,135,913 (GRCm39) I342N probably damaging Het
Calhm2 T C 19: 47,121,389 (GRCm39) D260G possibly damaging Het
Camk2a A G 18: 61,091,310 (GRCm39) E264G probably damaging Het
Ccdc146 T A 5: 21,524,543 (GRCm39) M270L probably benign Het
Cdc16 A G 8: 13,829,264 (GRCm39) T517A probably benign Het
Ces1g T C 8: 94,057,821 (GRCm39) H160R probably benign Het
Chst4 T C 8: 110,757,026 (GRCm39) N196S probably damaging Het
Ciz1 A T 2: 32,257,479 (GRCm39) N175Y probably damaging Het
Cyb5r4 G A 9: 86,909,093 (GRCm39) V57I probably damaging Het
Cyth3 A G 5: 143,670,181 (GRCm39) probably benign Het
Def6 A G 17: 28,439,154 (GRCm39) E255G probably damaging Het
Dhtkd1 T G 2: 5,916,681 (GRCm39) Q665P probably damaging Het
Dsg3 A C 18: 20,672,804 (GRCm39) D825A probably damaging Het
Eif3m T C 2: 104,835,345 (GRCm39) T242A probably benign Het
Emilin3 A G 2: 160,751,737 (GRCm39) F101L probably benign Het
Epha7 A G 4: 28,935,700 (GRCm39) probably null Het
Fbxo45 A T 16: 32,057,223 (GRCm39) Y224N probably damaging Het
Fhod3 A T 18: 25,223,161 (GRCm39) M836L possibly damaging Het
Fut4 C A 9: 14,662,506 (GRCm39) V263F probably damaging Het
Ggt1 C T 10: 75,415,104 (GRCm39) T206M probably benign Het
Gls T C 1: 52,227,858 (GRCm39) R79G probably damaging Het
Grhl1 T C 12: 24,631,514 (GRCm39) S156P probably benign Het
Ipo8 C T 6: 148,676,540 (GRCm39) S983N probably benign Het
Kcna7 C T 7: 45,058,868 (GRCm39) A385V probably damaging Het
Kpnb1 A T 11: 97,075,916 (GRCm39) L40Q probably damaging Het
Matn1 A T 4: 130,677,417 (GRCm39) S209C probably damaging Het
Mcc A G 18: 44,608,289 (GRCm39) I501T probably benign Het
Mdp1 A T 14: 55,896,832 (GRCm39) F104L probably damaging Het
Mib2 A T 4: 155,740,745 (GRCm39) N626K probably damaging Het
Mrgprh T C 17: 13,095,843 (GRCm39) S28P possibly damaging Het
Mup-ps23 T A 4: 61,774,386 (GRCm39) noncoding transcript Het
Myh15 A G 16: 49,003,322 (GRCm39) T1794A possibly damaging Het
Myo18a C G 11: 77,711,868 (GRCm39) P680A probably benign Het
Myom2 G T 8: 15,148,419 (GRCm39) D532Y possibly damaging Het
Ndufaf5 A G 2: 140,012,801 (GRCm39) N57S probably benign Het
Nectin3 C T 16: 46,278,550 (GRCm39) V282M probably damaging Het
Nup188 G T 2: 30,221,000 (GRCm39) D997Y probably damaging Het
Olfm3 T C 3: 114,916,454 (GRCm39) V462A probably damaging Het
Opcml A G 9: 28,724,694 (GRCm39) H164R possibly damaging Het
Or14a259 A T 7: 86,013,013 (GRCm39) C177* probably null Het
Or4c120 A T 2: 89,000,757 (GRCm39) F266L probably benign Het
Or8u9 A C 2: 86,002,050 (GRCm39) F37C probably damaging Het
Pacrg A G 17: 10,622,347 (GRCm39) I209T probably damaging Het
Pcf11 T C 7: 92,310,423 (GRCm39) M522V probably benign Het
Pck1 T A 2: 172,995,183 (GRCm39) M1K probably null Het
Pcm1 G T 8: 41,729,148 (GRCm39) E707* probably null Het
Pcsk5 G A 19: 17,632,213 (GRCm39) R318W probably damaging Het
Phf11d A T 14: 59,590,793 (GRCm39) M188K possibly damaging Het
Ppip5k2 A T 1: 97,668,262 (GRCm39) C615* probably null Het
Prkdc T A 16: 15,609,791 (GRCm39) S3132T probably damaging Het
Prl2c5 A T 13: 13,357,609 (GRCm39) probably benign Het
Prpsap2 A G 11: 61,631,826 (GRCm39) I177T possibly damaging Het
Rad50 A G 11: 53,541,346 (GRCm39) S1297P probably damaging Het
Rasip1 T A 7: 45,284,668 (GRCm39) N678K possibly damaging Het
Rubcn A G 16: 32,656,350 (GRCm39) S544P probably damaging Het
Rwdd2a A T 9: 86,456,453 (GRCm39) T210S possibly damaging Het
Scd2 A G 19: 44,291,479 (GRCm39) D306G probably damaging Het
Sf3b2 C T 19: 5,324,852 (GRCm39) D845N probably damaging Het
Sipa1l2 C A 8: 126,191,149 (GRCm39) C947F probably damaging Het
Slc12a1 A T 2: 125,067,951 (GRCm39) T1013S probably damaging Het
Slc18a2 A T 19: 59,275,799 (GRCm39) I461L probably benign Het
Slc1a6 C A 10: 78,637,756 (GRCm39) Y427* probably null Het
Slc30a4 A T 2: 122,531,319 (GRCm39) I231K probably damaging Het
Sos1 G T 17: 80,761,192 (GRCm39) A168D probably damaging Het
Spata31f1a T C 4: 42,851,161 (GRCm39) I332V probably benign Het
Sptb T C 12: 76,668,145 (GRCm39) S651G probably benign Het
Stk36 T C 1: 74,672,779 (GRCm39) L1007P probably damaging Het
Tek A T 4: 94,692,578 (GRCm39) N229Y probably damaging Het
Tep1 A G 14: 51,074,225 (GRCm39) F1887L possibly damaging Het
Tet1 A T 10: 62,713,988 (GRCm39) C602* probably null Het
Tnfrsf19 A G 14: 61,209,485 (GRCm39) S262P possibly damaging Het
Trim5 T C 7: 103,914,891 (GRCm39) I393V probably benign Het
Trpm6 A G 19: 18,830,951 (GRCm39) E1272G probably benign Het
Ttc21b A T 2: 66,018,670 (GRCm39) Y1246N probably damaging Het
Ttll3 T A 6: 113,375,738 (GRCm39) L151H probably damaging Het
U2surp C T 9: 95,366,496 (GRCm39) V470I probably benign Het
Ubr1 A T 2: 120,777,138 (GRCm39) Y276N probably benign Het
Uggt1 A G 1: 36,218,751 (GRCm39) S59P probably benign Het
Unc45a T C 7: 79,976,092 (GRCm39) T796A probably damaging Het
Unc5b C A 10: 60,614,719 (GRCm39) V193F possibly damaging Het
Upp1 G T 11: 9,079,590 (GRCm39) M50I probably benign Het
Vps18 C T 2: 119,124,386 (GRCm39) R438C probably damaging Het
Zfp715 T C 7: 42,948,760 (GRCm39) Y400C possibly damaging Het
Zfp955b T C 17: 33,521,496 (GRCm39) Y322H probably benign Het
Other mutations in Sema3b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00674:Sema3b APN 9 107,481,240 (GRCm39) critical splice donor site probably null
IGL02750:Sema3b APN 9 107,480,363 (GRCm39) missense probably benign 0.02
IGL02878:Sema3b APN 9 107,478,192 (GRCm39) missense probably damaging 0.97
IGL03004:Sema3b APN 9 107,480,114 (GRCm39) missense possibly damaging 0.72
IGL03026:Sema3b APN 9 107,479,262 (GRCm39) missense probably damaging 1.00
IGL03129:Sema3b APN 9 107,476,995 (GRCm39) unclassified probably benign
IGL03334:Sema3b APN 9 107,481,276 (GRCm39) missense probably damaging 1.00
R0384:Sema3b UTSW 9 107,478,165 (GRCm39) missense probably damaging 1.00
R0883:Sema3b UTSW 9 107,481,355 (GRCm39) missense possibly damaging 0.77
R3916:Sema3b UTSW 9 107,477,657 (GRCm39) missense probably damaging 1.00
R3971:Sema3b UTSW 9 107,477,567 (GRCm39) missense probably benign
R4212:Sema3b UTSW 9 107,480,597 (GRCm39) missense probably damaging 1.00
R4647:Sema3b UTSW 9 107,476,250 (GRCm39) missense possibly damaging 0.79
R4694:Sema3b UTSW 9 107,482,201 (GRCm39) missense probably benign 0.03
R4791:Sema3b UTSW 9 107,481,012 (GRCm39) missense probably damaging 1.00
R4853:Sema3b UTSW 9 107,479,266 (GRCm39) splice site probably null
R5305:Sema3b UTSW 9 107,480,536 (GRCm39) missense probably null 1.00
R5487:Sema3b UTSW 9 107,478,161 (GRCm39) missense probably damaging 1.00
R5745:Sema3b UTSW 9 107,478,628 (GRCm39) missense probably damaging 0.98
R5751:Sema3b UTSW 9 107,476,913 (GRCm39) missense probably benign
R6086:Sema3b UTSW 9 107,478,047 (GRCm39) missense probably damaging 1.00
R6306:Sema3b UTSW 9 107,478,119 (GRCm39) missense possibly damaging 0.88
R6594:Sema3b UTSW 9 107,476,025 (GRCm39) missense probably benign 0.01
R6816:Sema3b UTSW 9 107,477,549 (GRCm39) missense probably benign 0.08
R6833:Sema3b UTSW 9 107,480,515 (GRCm39) missense probably benign 0.04
R7320:Sema3b UTSW 9 107,478,141 (GRCm39) missense probably benign
R7448:Sema3b UTSW 9 107,480,162 (GRCm39) missense probably damaging 1.00
R7687:Sema3b UTSW 9 107,481,013 (GRCm39) missense probably damaging 1.00
R8839:Sema3b UTSW 9 107,478,552 (GRCm39) unclassified probably benign
R9090:Sema3b UTSW 9 107,476,154 (GRCm39) missense probably damaging 1.00
R9123:Sema3b UTSW 9 107,478,173 (GRCm39) missense possibly damaging 0.64
R9271:Sema3b UTSW 9 107,476,154 (GRCm39) missense probably damaging 1.00
R9442:Sema3b UTSW 9 107,478,957 (GRCm39) critical splice donor site probably null
R9682:Sema3b UTSW 9 107,481,013 (GRCm39) missense probably damaging 1.00
R9755:Sema3b UTSW 9 107,478,784 (GRCm39) missense probably damaging 1.00
Z1088:Sema3b UTSW 9 107,476,233 (GRCm39) splice site probably null
Z1176:Sema3b UTSW 9 107,476,838 (GRCm39) missense possibly damaging 0.89
Predicted Primers PCR Primer
(F):5'- TCAGCATATCCTGGCTCCAAGACC -3'
(R):5'- GACTCCTTATGACCCAAGGCATCG -3'

Sequencing Primer
(F):5'- GCTCAAAGACTCCTGCCTG -3'
(R):5'- TGTATTCTGGGGTGACAGCA -3'
Posted On 2013-04-24