Incidental Mutation 'R1221:Sema3a'
ID 100076
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 039290-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.947) question?
Stock # R1221 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 13175381-13652533 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 13566190 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 158 (Q158R)
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 benign
Transcript: ENSMUST00000030714
AA Change: Q158R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: Q158R

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 benign
Transcript: ENSMUST00000095012
AA Change: Q158R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: Q158R

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 benign
Transcript: ENSMUST00000137798
AA Change: Q158R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: Q158R

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 94.0%
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aak1 T C 6: 86,942,460 (GRCm39) S668P unknown Het
Anks1 A G 17: 28,269,616 (GRCm39) Q770R possibly damaging Het
Apc2 G A 10: 80,142,214 (GRCm39) V378I probably damaging Het
Apeh A G 9: 107,969,808 (GRCm39) V184A probably benign Het
AU018091 A G 7: 3,208,717 (GRCm39) F404S probably damaging Het
Bap1 T C 14: 30,979,608 (GRCm39) L537P probably damaging Het
Bhlha15 A G 5: 144,128,341 (GRCm39) Y151C probably damaging Het
Bmp8b A T 4: 123,008,504 (GRCm39) T157S probably damaging Het
Btbd1 G T 7: 81,468,005 (GRCm39) H172N possibly damaging Het
C1rl A G 6: 124,470,940 (GRCm39) R83G probably benign Het
Cep104 A G 4: 154,072,902 (GRCm39) T387A probably benign Het
Cfi A T 3: 129,666,618 (GRCm39) Q447L probably damaging Het
Cimap1a G T 7: 140,428,296 (GRCm39) W10L probably damaging Het
Coq6 A G 12: 84,418,301 (GRCm39) E295G possibly damaging Het
Dclre1a T C 19: 56,519,700 (GRCm39) T978A possibly damaging Het
Dlc1 T C 8: 37,051,985 (GRCm39) D582G probably benign Het
Dlgap2 A G 8: 14,776,952 (GRCm39) T65A probably benign Het
Dock5 G A 14: 67,996,610 (GRCm39) S1711L probably benign Het
Drc3 A C 11: 60,275,052 (GRCm39) I338L probably benign Het
Dsc1 A T 18: 20,247,599 (GRCm39) C5* probably null Het
F5 A G 1: 163,989,368 (GRCm39) Y90C probably damaging Het
Gdf10 G A 14: 33,654,710 (GRCm39) A406T probably benign Het
Gm136 G T 4: 34,744,127 (GRCm39) A239E possibly damaging Het
Gm4952 A T 19: 12,601,059 (GRCm39) D93V possibly damaging Het
Gramd1c T C 16: 43,810,227 (GRCm39) T454A possibly damaging Het
Gstm6 A G 3: 107,848,418 (GRCm39) I58T probably damaging Het
Kdm3b C T 18: 34,941,298 (GRCm39) S263L possibly damaging Het
Kdm5b G C 1: 134,526,829 (GRCm39) S317T probably damaging Het
Myo15b A G 11: 115,777,546 (GRCm39) R71G possibly damaging Het
Nlrp1b G A 11: 71,072,290 (GRCm39) P518S probably benign Het
Nme5 A T 18: 34,704,575 (GRCm39) I90N probably damaging Het
Nrxn1 T A 17: 90,950,722 (GRCm39) T478S probably damaging Het
Or8g22 A C 9: 38,958,483 (GRCm39) D77E probably damaging Het
Osmr G A 15: 6,853,042 (GRCm39) Q617* probably null Het
Pcsk5 T C 19: 17,814,512 (GRCm39) D2G possibly damaging Het
Pdpn G A 4: 143,000,608 (GRCm39) R75C probably damaging Het
Pidd1 A T 7: 141,018,725 (GRCm39) F842Y probably damaging Het
Resf1 T A 6: 149,227,719 (GRCm39) V255E probably benign Het
Setbp1 T A 18: 78,899,798 (GRCm39) R1290W probably damaging Het
Slc20a1 G A 2: 129,050,324 (GRCm39) G494D probably benign Het
Spag17 A G 3: 99,889,584 (GRCm39) E151G possibly damaging Het
Stt3b A G 9: 115,086,567 (GRCm39) F351L probably benign Het
Tas1r2 A G 4: 139,396,436 (GRCm39) M592V probably benign Het
Tbcd A G 11: 121,387,909 (GRCm39) T347A probably benign Het
Tmem109 C A 19: 10,851,733 (GRCm39) R37L possibly damaging Het
Tmem67 G A 4: 12,045,871 (GRCm39) S862L possibly damaging Het
Ttn T A 2: 76,781,857 (GRCm39) D1017V probably damaging Het
Zfp646 G A 7: 127,482,292 (GRCm39) G1490S probably benign Het
Zfyve16 T C 13: 92,644,813 (GRCm39) S1130G possibly 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
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
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
Predicted Primers PCR Primer
(F):5'- CCCAAGAGCCCTTTGTATATGGCATAG -3'
(R):5'- GTGCAATGATTCGGCCAACCATC -3'

Sequencing Primer
(F):5'- ATATGGCATAGATGTGCTTAGCTC -3'
(R):5'- GGACTGTTTCCCTGAACATGAC -3'
Posted On 2014-01-15