Incidental Mutation 'IGL02739:Sema3a'
ID 305797
Institutional Source Australian Phenomics Network (link to record)
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
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # IGL02739
Quality Score
Status
Chromosome 5
Chromosomal Location 13175381-13652533 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 13501128 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 57 (Y57C)
Ref Sequence ENSEMBL: ENSMUSP00000122621 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030714] [ENSMUST00000095012] [ENSMUST00000125629] [ENSMUST00000137798] [ENSMUST00000141968]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000030714
AA Change: Y57C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: Y57C

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 damaging
Transcript: ENSMUST00000095012
AA Change: Y57C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: Y57C

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 damaging
Transcript: ENSMUST00000125629
AA Change: Y57C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000121710
Gene: ENSMUSG00000028883
AA Change: Y57C

DomainStartEndE-ValueType
PDB:4GZA|G 20 72 1e-30 PDB
Predicted Effect probably damaging
Transcript: ENSMUST00000137798
AA Change: Y57C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: Y57C

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 damaging
Transcript: ENSMUST00000141968
AA Change: Y57C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000122621
Gene: ENSMUSG00000028883
AA Change: Y57C

DomainStartEndE-ValueType
PDB:4GZA|G 20 62 3e-23 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195907
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200073
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 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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aasdh A T 5: 77,026,364 (GRCm39) C887S possibly damaging Het
Adamdec1 C A 14: 68,807,605 (GRCm39) E352* probably null Het
Bglap2 A T 3: 88,285,319 (GRCm39) probably null Het
Bsn A T 9: 107,989,745 (GRCm39) H2002Q probably benign Het
Chtop T A 3: 90,409,557 (GRCm39) Q165L possibly damaging Het
Clcn1 A T 6: 42,263,714 (GRCm39) probably null Het
Ctsr T C 13: 61,309,658 (GRCm39) T184A probably benign Het
Defb36 T C 2: 152,446,439 (GRCm39) L11P unknown Het
Dock8 A G 19: 25,165,852 (GRCm39) E1912G probably damaging Het
Dpp3 A G 19: 4,973,756 (GRCm39) Y106H probably damaging Het
Epas1 A G 17: 87,112,710 (GRCm39) T103A probably damaging Het
Epcam A T 17: 87,947,922 (GRCm39) T131S probably benign Het
Fam169a A G 13: 97,230,563 (GRCm39) probably benign Het
Gh T A 11: 106,192,559 (GRCm39) probably benign Het
Kif20a A T 18: 34,761,996 (GRCm39) K399* probably null Het
Lrp1b A G 2: 41,388,227 (GRCm39) I466T probably damaging Het
Nlk A G 11: 78,465,677 (GRCm39) V409A probably benign Het
Nomo1 A G 7: 45,693,731 (GRCm39) probably null Het
Nr2c1 T A 10: 93,992,834 (GRCm39) M16K probably damaging Het
Nxph2 A T 2: 23,289,912 (GRCm39) Q88L probably benign Het
Or51a39 A G 7: 102,363,521 (GRCm39) I33T possibly damaging Het
Pkdrej T A 15: 85,703,895 (GRCm39) R680S probably benign Het
Pkhd1l1 A T 15: 44,404,346 (GRCm39) N2325I probably benign Het
Pnliprp2 T C 19: 58,748,941 (GRCm39) probably null Het
Ppp1r42 T A 1: 10,039,078 (GRCm39) K347N probably benign Het
Prtg T C 9: 72,758,867 (GRCm39) V407A possibly damaging Het
Psmb8 C A 17: 34,419,728 (GRCm39) S194* probably null Het
Rnf214 T C 9: 45,780,772 (GRCm39) I406V probably benign Het
Rreb1 C T 13: 38,077,797 (GRCm39) S3L probably damaging Het
Sdad1 C T 5: 92,437,931 (GRCm39) A539T probably benign Het
Susd5 A G 9: 113,925,101 (GRCm39) E328G possibly damaging Het
Syngr3 T C 17: 24,905,372 (GRCm39) T175A probably damaging Het
Tcf20 T A 15: 82,740,281 (GRCm39) Q390L probably damaging Het
Tex15 A G 8: 34,071,721 (GRCm39) T2423A possibly damaging Het
Tlr1 T C 5: 65,084,469 (GRCm39) N36S probably benign Het
Uchl4 C T 9: 64,142,819 (GRCm39) T100M probably damaging Het
Uhrf1 A G 17: 56,612,129 (GRCm39) K11R probably benign Het
Vps13b T A 15: 35,880,046 (GRCm39) D3040E probably damaging Het
Wdr62 A T 7: 29,941,885 (GRCm39) Y640* probably null Het
Zkscan17 T G 11: 59,394,352 (GRCm39) E83A probably damaging 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
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
R6132:Sema3a UTSW 5 13,573,142 (GRCm39) critical splice donor site probably null
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
Posted On 2015-04-16