Incidental Mutation 'IGL02676:Sema3d'
ID 303130
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Sema3d
Ensembl Gene ENSMUSG00000040254
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
Synonyms 4631426B19Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # IGL02676
Quality Score
Status
Chromosome 5
Chromosomal Location 12433352-12638915 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 12620945 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Leucine at position 517 (Q517L)
Ref Sequence ENSEMBL: ENSMUSP00000142453 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927]
AlphaFold Q8BH34
Predicted Effect probably benign
Transcript: ENSMUST00000030868
AA Change: Q517L

PolyPhen 2 Score 0.335 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Q517L

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
Predicted Effect probably benign
Transcript: ENSMUST00000197927
AA Change: Q517L

PolyPhen 2 Score 0.376 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: Q517L

DomainStartEndE-ValueType
signal peptide 1 37 N/A INTRINSIC
Sema 70 515 1e-209 SMART
PSI 533 585 8.5e-16 SMART
Blast:Sema 590 622 1e-9 BLAST
Coding Region Coverage
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 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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Apc G A 18: 34,448,687 (GRCm39) S1827N probably damaging Het
Atrnl1 T A 19: 57,680,316 (GRCm39) C739S probably damaging Het
Cep350 T C 1: 155,737,977 (GRCm39) E2622G possibly damaging Het
Chd5 C T 4: 152,440,530 (GRCm39) probably benign Het
Chst11 T A 10: 83,027,563 (GRCm39) L330Q probably damaging Het
Clcnka A T 4: 141,120,094 (GRCm39) V275E probably damaging Het
Clip4 G A 17: 72,135,616 (GRCm39) S456N probably damaging Het
Cmya5 A T 13: 93,229,361 (GRCm39) I1909N probably damaging Het
Cyp26b1 A G 6: 84,553,626 (GRCm39) I176T probably damaging Het
Dst A G 1: 34,346,668 (GRCm39) R7717G probably damaging Het
Eml2 C T 7: 18,918,846 (GRCm39) R99* probably null Het
Fibin T C 2: 110,192,929 (GRCm39) Q71R probably benign Het
Fsip2 T G 2: 82,812,501 (GRCm39) I2940S possibly damaging Het
Gabrb3 G T 7: 57,241,112 (GRCm39) probably benign Het
Gfra1 G A 19: 58,441,787 (GRCm39) T48I probably damaging Het
Gm6483 C T 8: 19,743,675 (GRCm39) noncoding transcript Het
Hdgfl1 G A 13: 26,953,348 (GRCm39) R242C possibly damaging Het
Hmcn1 T C 1: 150,494,760 (GRCm39) T4110A probably benign Het
Lama2 T G 10: 26,994,489 (GRCm39) M1807L probably benign Het
Larp4 T C 15: 99,888,302 (GRCm39) V113A possibly damaging Het
Mkx T C 18: 7,000,640 (GRCm39) T101A probably benign Het
Nfe2l1 A G 11: 96,718,491 (GRCm39) F15L probably damaging Het
Nherf2 A T 17: 24,860,930 (GRCm39) V204E probably damaging Het
Nif3l1 G A 1: 58,494,895 (GRCm39) probably null Het
Nop14 A G 5: 34,796,565 (GRCm39) V764A probably damaging Het
Nosip C A 7: 44,726,752 (GRCm39) A259E probably damaging Het
Ntn5 T C 7: 45,341,300 (GRCm39) probably benign Het
Or9g20 T C 2: 85,629,934 (GRCm39) I227V possibly damaging Het
Phospho1 G A 11: 95,721,714 (GRCm39) G128D probably damaging Het
Ppp4r3a G A 12: 101,008,770 (GRCm39) T703M probably benign Het
Pramel21 T C 4: 143,342,667 (GRCm39) F258S possibly damaging Het
Pramel58 A G 5: 94,831,730 (GRCm39) T246A possibly damaging Het
Prdm8 G A 5: 98,334,418 (GRCm39) E662K probably damaging Het
Ralgapa1 A G 12: 55,723,202 (GRCm39) S1775P probably damaging Het
Rapgef6 T C 11: 54,540,172 (GRCm39) probably benign Het
Rasef T C 4: 73,677,966 (GRCm39) T87A possibly damaging Het
Scrn3 A G 2: 73,160,215 (GRCm39) Q286R probably benign Het
Taf6l T C 19: 8,752,413 (GRCm39) Y425C probably damaging Het
Tbk1 T C 10: 121,403,985 (GRCm39) N254S possibly damaging Het
Tcf3 C T 10: 80,256,925 (GRCm39) G64R probably damaging Het
Tmco4 T C 4: 138,750,380 (GRCm39) probably null Het
Trappc11 A G 8: 47,946,448 (GRCm39) probably benign Het
Vmn1r19 A T 6: 57,382,025 (GRCm39) I193F possibly damaging Het
Vmn2r14 G A 5: 109,367,882 (GRCm39) T370I probably benign Het
Vmn2r65 T A 7: 84,589,381 (GRCm39) H845L possibly damaging Het
Vmn2r98 A T 17: 19,285,521 (GRCm39) T114S probably benign Het
Zfp280d A T 9: 72,242,356 (GRCm39) R661S probably damaging Het
Zranb1 T C 7: 132,568,410 (GRCm39) I356T probably benign 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
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
R4063:Sema3d UTSW 5 12,635,091 (GRCm39) missense probably benign 0.25
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
Posted On 2015-04-16