Incidental Mutation 'R1657:Sema3d'
ID 186453
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 039693-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.188) question?
Stock # R1657 (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 G at 12634941 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 669 (E669G)
Ref Sequence ENSEMBL: ENSMUSP00000030868 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030868]
AlphaFold Q8BH34
Predicted Effect possibly damaging
Transcript: ENSMUST00000030868
AA Change: E669G

PolyPhen 2 Score 0.823 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: E669G

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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T G 11: 84,154,910 (GRCm39) D988E probably benign Het
Als2 A G 1: 59,219,760 (GRCm39) V1185A probably damaging Het
Amdhd2 A G 17: 24,375,029 (GRCm39) V391A probably damaging Het
Armh4 G C 14: 50,011,017 (GRCm39) T230S probably damaging Het
Caprin1 A T 2: 103,599,851 (GRCm39) V608E probably damaging Het
Celsr3 T A 9: 108,720,151 (GRCm39) C2512* probably null Het
Cfl1 A T 19: 5,543,583 (GRCm39) R187W probably damaging Het
Cgnl1 C T 9: 71,633,226 (GRCm39) V42I probably damaging Het
Chd2 A G 7: 73,130,178 (GRCm39) Y826H probably damaging Het
Col9a2 C A 4: 120,898,171 (GRCm39) P28T unknown Het
Cyp3a44 G A 5: 145,716,553 (GRCm39) P346S probably damaging Het
Dact2 A G 17: 14,418,252 (GRCm39) V151A probably benign Het
Dhx29 T C 13: 113,089,377 (GRCm39) I716T probably damaging Het
Entrep1 C A 19: 23,952,999 (GRCm39) C437F probably damaging Het
Esam T C 9: 37,448,917 (GRCm39) S342P probably damaging Het
Fer1l4 A G 2: 155,877,518 (GRCm39) V1053A possibly damaging Het
Grk3 A G 5: 113,114,848 (GRCm39) F124S probably damaging Het
H2-DMa G A 17: 34,356,373 (GRCm39) probably null Het
Hsd3b5 T A 3: 98,527,036 (GRCm39) I137F possibly damaging Het
Itgav A T 2: 83,632,123 (GRCm39) I902F probably benign Het
Itsn1 G T 16: 91,706,111 (GRCm39) C179F probably damaging Het
Kcnh8 G A 17: 53,146,153 (GRCm39) R347H probably damaging Het
Kif9 T C 9: 110,319,034 (GRCm39) M166T possibly damaging Het
Kmt5c C T 7: 4,749,453 (GRCm39) Q324* probably null Het
Lcn9 G A 2: 25,714,722 (GRCm39) E154K probably benign Het
Mfge8 A T 7: 78,791,521 (GRCm39) L227Q probably benign Het
Mroh2b A T 15: 4,960,525 (GRCm39) R753* probably null Het
Mtif2 G A 11: 29,490,721 (GRCm39) R475Q probably benign Het
Nln C T 13: 104,173,455 (GRCm39) V584I possibly damaging Het
Nr2e3 T C 9: 59,856,050 (GRCm39) E129G probably benign Het
Ocstamp T C 2: 165,239,436 (GRCm39) D250G probably damaging Het
Or1a1 A T 11: 74,086,722 (GRCm39) H131L probably damaging Het
Or52n4b T C 7: 108,144,584 (GRCm39) I284T possibly damaging Het
Or8k27 A C 2: 86,275,562 (GRCm39) L255V probably damaging Het
Pld1 A T 3: 28,125,336 (GRCm39) I417L probably benign Het
Polr1a A T 6: 71,918,519 (GRCm39) K692N probably damaging Het
Qsox2 A T 2: 26,110,759 (GRCm39) Y152* probably null Het
Rpap1 T C 2: 119,614,259 (GRCm39) D46G possibly damaging Het
Rpe65 A G 3: 159,320,085 (GRCm39) T246A probably damaging Het
Scn5a T C 9: 119,391,446 (GRCm39) D82G probably damaging Het
Serpinb6c T C 13: 34,064,209 (GRCm39) N282S probably benign Het
Snap47 A T 11: 59,319,596 (GRCm39) S181T probably benign Het
Snx9 A C 17: 5,968,711 (GRCm39) T336P possibly damaging Het
Sphkap G A 1: 83,255,236 (GRCm39) R838* probably null Het
Terb1 A T 8: 105,215,123 (GRCm39) D284E possibly damaging Het
Tmem266 C T 9: 55,325,292 (GRCm39) A153V probably damaging Het
Trappc2b T C 11: 51,576,505 (GRCm39) Q131R probably benign Het
Ttn T C 2: 76,573,148 (GRCm39) E25915G possibly damaging Het
Tubal3 A G 13: 3,983,011 (GRCm39) T264A possibly damaging Het
Vldlr G A 19: 27,223,070 (GRCm39) R747Q probably benign Het
Zc3h8 G T 2: 128,771,877 (GRCm39) probably benign Het
Zfp184 C T 13: 22,143,443 (GRCm39) T383M probably damaging Het
Zfp455 T C 13: 67,346,703 (GRCm39) F38S possibly damaging Het
Zfp746 A G 6: 48,059,108 (GRCm39) V167A possibly damaging Het
Zfp985 T A 4: 147,668,567 (GRCm39) N478K 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
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
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'- AGCAGGTTATATCTTGGGGACTACTACC -3'
(R):5'- GTACTGGTCCAGGCTGAAGTTCG -3'

Sequencing Primer
(F):5'- tctttctttcttcctttcttccttc -3'
(R):5'- TCGGGCTGCTAAGGATTTG -3'
Posted On 2014-05-09