Incidental Mutation 'R0930:Sema3d'
ID 80727
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
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # R0930 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 12433352-12638915 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 12513183 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Alanine at position 51 (D51A)
Ref Sequence ENSEMBL: ENSMUSP00000142453 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927]
AlphaFold Q8BH34
Predicted Effect possibly damaging
Transcript: ENSMUST00000030868
AA Change: D51A

PolyPhen 2 Score 0.467 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: D51A

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: ENSMUST00000196618
Predicted Effect possibly damaging
Transcript: ENSMUST00000197927
AA Change: D51A

PolyPhen 2 Score 0.690 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: D51A

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
Meta Mutation Damage Score 0.4737 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.5%
  • 20x: 95.5%
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg8 G T 17: 84,990,705 (GRCm39) V16L probably benign Het
Adamts18 A T 8: 114,432,028 (GRCm39) probably null Het
Agpat4 A T 17: 12,417,723 (GRCm39) E88V probably damaging Het
Ahcyl2 A C 6: 29,870,627 (GRCm39) probably null Het
Ankrd2 T A 19: 42,032,292 (GRCm39) probably null Het
Anxa6 A T 11: 54,885,214 (GRCm39) probably null Het
Bpi A G 2: 158,103,346 (GRCm39) I114V possibly damaging Het
Cacna1c A T 6: 118,652,857 (GRCm39) I772N probably damaging Het
Cacna2d1 A G 5: 16,570,860 (GRCm39) N1045D possibly damaging Het
Caprin2 T C 6: 148,785,009 (GRCm39) probably null Het
Cars1 T A 7: 143,124,307 (GRCm39) H373L probably damaging Het
Ccdc191 G T 16: 43,751,618 (GRCm39) G316V probably damaging Het
Cd244a T A 1: 171,404,801 (GRCm39) probably null Het
Ces1a C T 8: 93,749,044 (GRCm39) D456N probably benign Het
Cul3 A T 1: 80,267,835 (GRCm39) M102K probably damaging Het
Dact1 A G 12: 71,365,234 (GRCm39) R672G probably damaging Het
Dapk1 T C 13: 60,905,262 (GRCm39) F991L probably benign Het
Dlg5 G A 14: 24,185,645 (GRCm39) P1920L probably damaging Het
Eme2 G A 17: 25,111,892 (GRCm39) S263F probably damaging Het
Exosc4 A G 15: 76,211,734 (GRCm39) I14M probably benign Het
Ezr G A 17: 7,021,398 (GRCm39) R180* probably null Het
Fcgbpl1 A T 7: 27,839,555 (GRCm39) Y456F probably damaging Het
Fyb1 A T 15: 6,668,309 (GRCm39) I501F probably damaging Het
Hdac5 G T 11: 102,095,472 (GRCm39) P383Q probably benign Het
Hmx3 A T 7: 131,144,813 (GRCm39) H41L probably benign Het
Krt36 A G 11: 99,994,225 (GRCm39) F284S probably damaging Het
L1td1 A G 4: 98,625,862 (GRCm39) N686D probably damaging Het
Lsamp G A 16: 41,709,327 (GRCm39) G86S probably benign Het
Myh8 A G 11: 67,196,824 (GRCm39) E1819G possibly damaging Het
Myo7a A T 7: 97,747,463 (GRCm39) I129N probably damaging Het
Nckap1 A T 2: 80,384,593 (GRCm39) C114S probably benign Het
Nphp4 T G 4: 152,622,512 (GRCm39) L599R probably benign Het
Nrcam A G 12: 44,596,667 (GRCm39) I301V probably benign Het
Or6b2b A G 1: 92,419,127 (GRCm39) S117P possibly damaging Het
Os9 C T 10: 126,932,924 (GRCm39) R547Q probably damaging Het
Oxtr A T 6: 112,466,598 (GRCm39) probably null Het
Pgm2 A T 5: 64,269,490 (GRCm39) I526F possibly damaging Het
Plekho2 T C 9: 65,464,105 (GRCm39) D248G possibly damaging Het
Rab43 A T 6: 87,769,752 (GRCm39) Y151* probably null Het
Rbm19 A G 5: 120,264,269 (GRCm39) E343G probably benign Het
Rel A T 11: 23,692,439 (GRCm39) D531E probably benign Het
Rfx4 T A 10: 84,704,291 (GRCm39) V262E probably damaging Het
Ryr3 A G 2: 112,672,178 (GRCm39) L1431P probably damaging Het
Sdk2 A G 11: 113,729,271 (GRCm39) I1102T probably benign Het
Sh2d4a T A 8: 68,787,775 (GRCm39) F294I probably damaging Het
Slc3a1 A G 17: 85,367,171 (GRCm39) T453A probably benign Het
Sod1 A G 16: 90,022,071 (GRCm39) D93G probably benign Het
Sptan1 A G 2: 29,906,040 (GRCm39) N1662S probably damaging Het
Stxbp4 A C 11: 90,512,526 (GRCm39) M1R probably null Het
Tbc1d7 A T 13: 43,318,812 (GRCm39) Y108* probably null Het
Ticam1 A T 17: 56,577,226 (GRCm39) V623D unknown Het
Ticam1 A G 17: 56,578,687 (GRCm39) L136P probably damaging Het
Tjap1 A C 17: 46,569,455 (GRCm39) W512G possibly damaging Het
Unc80 A T 1: 66,549,800 (GRCm39) Q686L possibly damaging Het
Wdr45b A T 11: 121,221,040 (GRCm39) F213I probably damaging Het
Xdh A C 17: 74,230,077 (GRCm39) W285G probably benign Het
Zfp646 C T 7: 127,482,982 (GRCm39) Q1500* probably null 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
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
Predicted Primers PCR Primer
(F):5'- GGTTAGGAGGAGAGCCAAGATACTGTAATA -3'
(R):5'- GCACACAGAAGAAATTCAGTGAATCTACCAA -3'

Sequencing Primer
(F):5'- tttataCACAGAATAGGGTTAAGCAC -3'
(R):5'- GAAATTCAGTGAATCTACCAATGATG -3'
Posted On 2013-11-07