Incidental Mutation 'R6132:Sema3a'
ID 487171
Institutional Source Beutler Lab
Gene Symbol Sema3a
Ensembl Gene ENSMUSG00000028883
Gene Name sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
Synonyms Semad, collapsin-1, SemD, sema III, semaphorin III
MMRRC Submission 044279-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # R6132 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 13175381-13652533 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to G at 13573142 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000128153 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030714] [ENSMUST00000095012] [ENSMUST00000137798]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000030714
SMART Domains Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883

DomainStartEndE-ValueType
Sema 57 498 4.09e-219 SMART
PSI 516 568 3.03e-12 SMART
IG 583 669 3.54e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000095012
SMART Domains Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883

DomainStartEndE-ValueType
Sema 57 498 4.09e-219 SMART
PSI 516 568 3.03e-12 SMART
IG 583 669 3.54e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000137798
SMART Domains Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883

DomainStartEndE-ValueType
Sema 57 498 4.09e-219 SMART
PSI 516 568 3.03e-12 SMART
IG 583 669 3.54e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195907
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197609
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.9%
Validation Efficiency 96% (49/51)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit patterning abnormalities of sensory and sympathetic neurons, abnormal embryonic bones and cartilaginous structures, cardiac defects, and high postnatal mortality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca15 T C 7: 119,960,643 (GRCm39) Y702H probably benign Het
Adgrv1 G T 13: 81,654,195 (GRCm39) N2225K probably benign Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Alkbh5 G T 11: 60,428,821 (GRCm39) probably benign Het
Atp5mc1 A G 11: 95,965,850 (GRCm39) M1T probably null Het
Crebrf C T 17: 26,982,377 (GRCm39) P588S probably benign Het
Ctsr A C 13: 61,309,582 (GRCm39) probably null Het
Cyp2c68 A G 19: 39,691,858 (GRCm39) V355A possibly damaging Het
Ddx52 A G 11: 83,850,283 (GRCm39) K555E possibly damaging Het
Depdc5 T A 5: 33,067,811 (GRCm39) S410T probably damaging Het
Dhx30 A T 9: 109,914,847 (GRCm39) I884N probably damaging Het
Dlg1 A T 16: 31,655,059 (GRCm39) N518I possibly damaging Het
Dnah12 T A 14: 26,439,066 (GRCm39) I506N probably damaging Het
Efcab6 A G 15: 83,917,173 (GRCm39) L129P probably damaging Het
Erap1 A G 13: 74,808,401 (GRCm39) N38D probably benign Het
Esf1 A G 2: 140,001,699 (GRCm39) F383L probably benign Het
Exoc4 A G 6: 33,735,033 (GRCm39) E550G probably damaging Het
Fbxo44 G A 4: 148,240,565 (GRCm39) T221I probably benign Het
Gal3st2b A T 1: 93,867,688 (GRCm39) M112L possibly damaging Het
Golph3l C G 3: 95,499,145 (GRCm39) P96A probably benign Het
Gprc6a T A 10: 51,491,356 (GRCm39) I727F possibly damaging Het
Grin3b T C 10: 79,812,274 (GRCm39) L479P probably damaging Het
Kdm5a C T 6: 120,351,892 (GRCm39) H161Y probably damaging Het
Lman2 A G 13: 55,510,038 (GRCm39) S73P probably benign Het
Map3k19 T C 1: 127,778,213 (GRCm39) N4S possibly damaging Het
Mkln1 G A 6: 31,408,155 (GRCm39) V161M probably damaging Het
Mmel1 C T 4: 154,979,475 (GRCm39) H728Y probably damaging Het
Nova2 G A 7: 18,691,794 (GRCm39) A244T unknown Het
Nrcam T A 12: 44,617,007 (GRCm39) Y668N probably damaging Het
Oacyl G T 18: 65,859,426 (GRCm39) G255W probably damaging Het
Omd A C 13: 49,743,843 (GRCm39) I298L probably damaging Het
Or5ac19 A G 16: 59,089,367 (GRCm39) V221A probably damaging Het
Or5ak24 A T 2: 85,260,490 (GRCm39) S228T probably benign Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Otor A T 2: 142,920,520 (GRCm39) D34V probably damaging Het
Otx1 A T 11: 21,949,406 (GRCm39) L24H probably damaging Het
Pwwp2a A G 11: 43,596,455 (GRCm39) Y540C probably damaging Het
Rttn T A 18: 89,133,770 (GRCm39) probably null Het
S1pr4 G A 10: 81,335,030 (GRCm39) A148V probably benign Het
Scn10a C T 9: 119,442,761 (GRCm39) V1495M possibly damaging Het
Sel1l3 T C 5: 53,357,531 (GRCm39) K154E possibly damaging Het
Slf2 T A 19: 44,949,300 (GRCm39) N870K possibly damaging Het
Spmip6 C T 4: 41,517,160 (GRCm39) M1I probably null Het
Syne2 T C 12: 75,991,921 (GRCm39) V1962A probably benign Het
Tarbp1 T A 8: 127,161,548 (GRCm39) I1219F probably benign Het
Tet1 A C 10: 62,649,079 (GRCm39) C173W probably damaging Het
Tnn A G 1: 159,973,641 (GRCm39) F242S probably damaging Het
Tollip A G 7: 141,443,334 (GRCm39) S174P probably benign Het
Tsr3 G T 17: 25,460,835 (GRCm39) D234Y probably null Het
Vmn2r106 T C 17: 20,488,666 (GRCm39) T578A probably benign Het
Zfp457 G T 13: 67,441,360 (GRCm39) S309* probably null Het
Other mutations in Sema3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01022:Sema3a APN 5 13,523,433 (GRCm39) missense probably damaging 1.00
IGL01783:Sema3a APN 5 13,611,767 (GRCm39) missense probably damaging 1.00
IGL02423:Sema3a APN 5 13,615,776 (GRCm39) missense probably damaging 1.00
IGL02728:Sema3a APN 5 13,615,881 (GRCm39) missense probably damaging 1.00
IGL02739:Sema3a APN 5 13,501,128 (GRCm39) missense probably damaging 1.00
IGL02987:Sema3a APN 5 13,615,863 (GRCm39) missense probably damaging 1.00
IGL03106:Sema3a APN 5 13,649,456 (GRCm39) missense probably damaging 1.00
R0055:Sema3a UTSW 5 13,450,004 (GRCm39) missense possibly damaging 0.92
R0334:Sema3a UTSW 5 13,607,268 (GRCm39) missense probably damaging 0.99
R0684:Sema3a UTSW 5 13,606,494 (GRCm39) critical splice acceptor site probably null
R0750:Sema3a UTSW 5 13,607,092 (GRCm39) critical splice donor site probably null
R1204:Sema3a UTSW 5 13,573,142 (GRCm39) critical splice donor site probably benign
R1221:Sema3a UTSW 5 13,566,190 (GRCm39) missense probably benign
R1484:Sema3a UTSW 5 13,523,407 (GRCm39) missense probably damaging 1.00
R1663:Sema3a UTSW 5 13,607,092 (GRCm39) critical splice donor site probably null
R2079:Sema3a UTSW 5 13,501,098 (GRCm39) missense possibly damaging 0.95
R4165:Sema3a UTSW 5 13,523,364 (GRCm39) critical splice acceptor site probably null
R4596:Sema3a UTSW 5 13,620,125 (GRCm39) missense probably damaging 1.00
R4867:Sema3a UTSW 5 13,501,208 (GRCm39) missense probably benign 0.05
R4904:Sema3a UTSW 5 13,631,066 (GRCm39) missense probably damaging 1.00
R5107:Sema3a UTSW 5 13,627,572 (GRCm39) nonsense probably null
R5327:Sema3a UTSW 5 13,649,357 (GRCm39) missense probably benign 0.25
R5343:Sema3a UTSW 5 13,523,373 (GRCm39) missense probably damaging 1.00
R5430:Sema3a UTSW 5 13,615,730 (GRCm39) missense probably damaging 0.97
R5604:Sema3a UTSW 5 13,523,487 (GRCm39) critical splice donor site probably null
R5774:Sema3a UTSW 5 13,573,131 (GRCm39) missense probably damaging 1.00
R6057:Sema3a UTSW 5 13,615,832 (GRCm39) missense probably damaging 1.00
R6110:Sema3a UTSW 5 13,630,969 (GRCm39) missense probably damaging 1.00
R6310:Sema3a UTSW 5 13,606,986 (GRCm39) missense probably damaging 1.00
R6754:Sema3a UTSW 5 13,649,243 (GRCm39) missense possibly damaging 0.94
R6788:Sema3a UTSW 5 13,647,584 (GRCm39) missense possibly damaging 0.95
R6878:Sema3a UTSW 5 13,505,511 (GRCm39) missense possibly damaging 0.88
R7411:Sema3a UTSW 5 13,566,230 (GRCm39) nonsense probably null
R7501:Sema3a UTSW 5 13,607,008 (GRCm39) missense probably damaging 1.00
R7514:Sema3a UTSW 5 13,573,093 (GRCm39) missense probably benign 0.03
R7531:Sema3a UTSW 5 13,615,805 (GRCm39) missense probably damaging 1.00
R7538:Sema3a UTSW 5 13,611,787 (GRCm39) missense probably benign 0.42
R7970:Sema3a UTSW 5 13,649,375 (GRCm39) missense possibly damaging 0.93
R8121:Sema3a UTSW 5 13,649,215 (GRCm39) missense probably damaging 1.00
R8283:Sema3a UTSW 5 13,450,030 (GRCm39) missense probably damaging 0.98
R8434:Sema3a UTSW 5 13,523,487 (GRCm39) critical splice donor site probably null
R8918:Sema3a UTSW 5 13,573,099 (GRCm39) missense probably damaging 1.00
R9500:Sema3a UTSW 5 13,615,854 (GRCm39) missense possibly damaging 0.88
X0064:Sema3a UTSW 5 13,631,066 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCCTGCTTTTAGGACCCAAGG -3'
(R):5'- TGGCCCAAAACAAATACTTCCTTAG -3'

Sequencing Primer
(F):5'- GCTTTTAGGACCCAAGGATGAAATAC -3'
(R):5'- TTCTCACACCCACAGTCAT -3'
Posted On 2017-10-10