Incidental Mutation 'R4063:Sema3d'
ID 315952
Institutional Source Beutler Lab
Gene Symbol Sema3d
Ensembl Gene ENSMUSG00000040254
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
Synonyms 4631426B19Rik
MMRRC Submission 041619-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # R4063 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 12433352-12638915 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 12635091 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 719 (I719N)
Ref Sequence ENSEMBL: ENSMUSP00000030868 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868]
AlphaFold Q8BH34
Predicted Effect probably benign
Transcript: ENSMUST00000030868
AA Change: I719N

PolyPhen 2 Score 0.252 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: I719N

DomainStartEndE-ValueType
transmembrane domain 16 35 N/A INTRINSIC
Sema 70 515 2.97e-207 SMART
PSI 533 585 2.03e-13 SMART
IG 598 682 1.39e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195923
Meta Mutation Damage Score 0.2932 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 97% (59/61)
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 like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700034J05Rik A T 6: 146,854,606 (GRCm39) F145L probably benign Het
Abcc9 T C 6: 142,551,645 (GRCm39) D1221G possibly damaging Het
Adamtsl4 T C 3: 95,584,864 (GRCm39) K935E probably benign Het
Ago4 A T 4: 126,409,655 (GRCm39) probably benign Het
Arhgef28 T C 13: 98,130,575 (GRCm39) D421G probably benign Het
Armh4 T A 14: 50,011,444 (GRCm39) M88L probably benign Het
Atl2 T C 17: 80,157,588 (GRCm39) *413W probably null Het
B4galt7 C A 13: 55,756,152 (GRCm39) probably null Het
Bltp3b A G 10: 89,651,917 (GRCm39) N247S probably benign Het
C8g A T 2: 25,389,425 (GRCm39) S147T probably damaging Het
Clstn3 A T 6: 124,426,792 (GRCm39) Y510N possibly damaging Het
Cnot2 A G 10: 116,373,301 (GRCm39) V34A possibly damaging Het
Cyb5d2 A T 11: 72,686,606 (GRCm39) probably benign Het
Dnah5 T C 15: 28,421,144 (GRCm39) I3827T probably damaging Het
Dnah7a G T 1: 53,464,376 (GRCm39) Q3672K probably benign Het
Dock1 A T 7: 134,717,021 (GRCm39) Y1219F possibly damaging Het
Espl1 A G 15: 102,221,424 (GRCm39) I944V probably damaging Het
Fat1 A T 8: 45,478,518 (GRCm39) E2521D probably benign Het
Gm10719 G T 9: 3,019,043 (GRCm39) W96L probably damaging Het
H2-M2 G A 17: 37,792,399 (GRCm39) H291Y probably damaging Het
Hmgcl T C 4: 135,686,035 (GRCm39) Y167H probably damaging Het
Il22ra2 A T 10: 19,502,400 (GRCm39) D73V possibly damaging Het
Incenp A T 19: 9,861,142 (GRCm39) M480K unknown Het
Irag1 G T 7: 110,522,984 (GRCm39) A359D probably benign Het
Kdm6a A G X: 18,117,114 (GRCm39) T266A probably benign Het
Lipf A G 19: 33,942,965 (GRCm39) N91S probably benign Het
M1ap A T 6: 82,980,756 (GRCm39) N214I probably damaging Het
Mast3 A G 8: 71,233,838 (GRCm39) V969A probably damaging Het
Mdga1 A G 17: 30,057,005 (GRCm39) C826R probably damaging Het
Msx1 C A 5: 37,981,365 (GRCm39) A105S probably benign Het
Or5ac23 A C 16: 59,149,243 (GRCm39) S210A probably benign Het
Otogl A T 10: 107,626,510 (GRCm39) D1451E probably benign Het
Otop2 G A 11: 115,220,201 (GRCm39) G347D probably damaging Het
Ppp1r13l A T 7: 19,103,978 (GRCm39) H153L probably benign Het
Pramel21 A G 4: 143,342,559 (GRCm39) D222G possibly damaging Het
Pramel29 T C 4: 143,935,265 (GRCm39) K161E possibly damaging Het
Proz A G 8: 13,114,621 (GRCm39) Y85C probably damaging Het
Prss50 A G 9: 110,687,480 (GRCm39) D141G probably benign Het
Rad54l2 T A 9: 106,597,613 (GRCm39) Q131L probably benign Het
Sdha A G 13: 74,472,077 (GRCm39) probably benign Het
Slc18b1 A T 10: 23,681,879 (GRCm39) I148L probably benign Het
Tacc2 G T 7: 130,330,852 (GRCm39) D2086Y probably damaging Het
Tchh T C 3: 93,354,298 (GRCm39) L1246P unknown Het
Tmprss11d T C 5: 86,457,177 (GRCm39) I161V probably benign Het
Trpc3 T C 3: 36,725,172 (GRCm39) D268G probably damaging Het
Trpm8 G A 1: 88,289,727 (GRCm39) R895H probably damaging Het
Txndc2 A G 17: 65,945,079 (GRCm39) I366T possibly damaging Het
Ugt2a3 T C 5: 87,484,725 (GRCm39) I100V probably benign Het
Upp1 C A 11: 9,081,709 (GRCm39) P82Q probably damaging Het
Vim A G 2: 13,584,827 (GRCm39) probably null Het
Vmn2r12 A T 5: 109,240,058 (GRCm39) N168K possibly damaging Het
Zdhhc14 G T 17: 5,802,983 (GRCm39) C362F probably damaging Het
Zfp292 A G 4: 34,810,863 (GRCm39) V727A probably damaging Het
Zswim5 G A 4: 116,735,177 (GRCm39) G174D unknown Het
Other mutations in Sema3d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00559:Sema3d APN 5 12,613,189 (GRCm39) missense probably benign 0.01
IGL00582:Sema3d APN 5 12,635,162 (GRCm39) missense probably damaging 1.00
IGL00661:Sema3d APN 5 12,555,806 (GRCm39) missense probably damaging 1.00
IGL00780:Sema3d APN 5 12,574,293 (GRCm39) missense probably damaging 1.00
IGL01531:Sema3d APN 5 12,591,047 (GRCm39) missense probably benign
IGL01957:Sema3d APN 5 12,613,282 (GRCm39) missense probably damaging 1.00
IGL02100:Sema3d APN 5 12,634,958 (GRCm39) missense probably benign 0.29
IGL02676:Sema3d APN 5 12,620,945 (GRCm39) missense probably benign 0.38
IGL02749:Sema3d APN 5 12,613,112 (GRCm39) splice site probably benign
IGL02827:Sema3d APN 5 12,635,085 (GRCm39) missense probably benign 0.04
IGL03325:Sema3d APN 5 12,513,189 (GRCm39) missense probably damaging 0.99
R0050:Sema3d UTSW 5 12,634,920 (GRCm39) missense probably benign 0.00
R0085:Sema3d UTSW 5 12,620,953 (GRCm39) missense probably benign 0.00
R0095:Sema3d UTSW 5 12,613,314 (GRCm39) missense probably damaging 1.00
R0157:Sema3d UTSW 5 12,558,104 (GRCm39) missense possibly damaging 0.95
R0328:Sema3d UTSW 5 12,498,042 (GRCm39) missense possibly damaging 0.48
R0924:Sema3d UTSW 5 12,513,183 (GRCm39) missense possibly damaging 0.69
R0930:Sema3d UTSW 5 12,513,183 (GRCm39) missense possibly damaging 0.69
R1609:Sema3d UTSW 5 12,591,023 (GRCm39) missense probably damaging 1.00
R1657:Sema3d UTSW 5 12,634,941 (GRCm39) missense possibly damaging 0.82
R1669:Sema3d UTSW 5 12,558,051 (GRCm39) splice site probably benign
R1795:Sema3d UTSW 5 12,634,854 (GRCm39) missense probably benign 0.02
R1861:Sema3d UTSW 5 12,547,570 (GRCm39) missense probably benign 0.00
R1889:Sema3d UTSW 5 12,534,988 (GRCm39) splice site probably null
R1895:Sema3d UTSW 5 12,623,810 (GRCm39) missense probably damaging 1.00
R1946:Sema3d UTSW 5 12,623,810 (GRCm39) missense probably damaging 1.00
R1975:Sema3d UTSW 5 12,634,965 (GRCm39) missense probably benign
R1975:Sema3d UTSW 5 12,613,285 (GRCm39) missense probably damaging 1.00
R2117:Sema3d UTSW 5 12,613,240 (GRCm39) missense probably benign
R2148:Sema3d UTSW 5 12,534,926 (GRCm39) missense probably damaging 0.99
R2276:Sema3d UTSW 5 12,592,549 (GRCm39) missense possibly damaging 0.63
R3761:Sema3d UTSW 5 12,621,004 (GRCm39) missense probably damaging 1.00
R4428:Sema3d UTSW 5 12,498,087 (GRCm39) missense probably benign 0.32
R4903:Sema3d UTSW 5 12,613,125 (GRCm39) missense probably benign 0.00
R4999:Sema3d UTSW 5 12,558,054 (GRCm39) splice site probably null
R5000:Sema3d UTSW 5 12,498,005 (GRCm39) missense probably benign 0.01
R5022:Sema3d UTSW 5 12,634,923 (GRCm39) missense probably damaging 1.00
R5186:Sema3d UTSW 5 12,634,875 (GRCm39) missense probably benign
R5584:Sema3d UTSW 5 12,620,954 (GRCm39) missense possibly damaging 0.73
R5584:Sema3d UTSW 5 12,615,975 (GRCm39) missense possibly damaging 0.49
R6270:Sema3d UTSW 5 12,498,074 (GRCm39) missense probably benign
R6368:Sema3d UTSW 5 12,620,980 (GRCm39) missense probably damaging 1.00
R6426:Sema3d UTSW 5 12,613,231 (GRCm39) missense probably damaging 1.00
R6750:Sema3d UTSW 5 12,635,067 (GRCm39) nonsense probably null
R7403:Sema3d UTSW 5 12,547,551 (GRCm39) missense probably damaging 0.97
R7450:Sema3d UTSW 5 12,634,901 (GRCm39) nonsense probably null
R7470:Sema3d UTSW 5 12,558,152 (GRCm39) missense probably damaging 1.00
R7548:Sema3d UTSW 5 12,627,783 (GRCm39) missense unknown
R7593:Sema3d UTSW 5 12,558,112 (GRCm39) missense probably benign 0.02
R7683:Sema3d UTSW 5 12,623,823 (GRCm39) nonsense probably null
R8155:Sema3d UTSW 5 12,498,148 (GRCm39) critical splice donor site probably null
R8442:Sema3d UTSW 5 12,592,608 (GRCm39) missense probably damaging 0.99
R8725:Sema3d UTSW 5 12,555,822 (GRCm39) missense probably damaging 1.00
R8754:Sema3d UTSW 5 12,603,191 (GRCm39) critical splice donor site probably null
R9293:Sema3d UTSW 5 12,603,181 (GRCm39) missense probably damaging 1.00
R9771:Sema3d UTSW 5 12,613,207 (GRCm39) missense probably damaging 0.99
Z1176:Sema3d UTSW 5 12,635,026 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TATTACTGCAAAGCACAGGAGC -3'
(R):5'- GACATTATTTGTGCAGGCAGG -3'

Sequencing Primer
(F):5'- GCACAGGAGCACACTTTCATC -3'
(R):5'- GTGCAGGCAGGTAAATAATTCCCTC -3'
Posted On 2015-05-15