Incidental Mutation 'IGL02076:Sema4a'
ID 185992
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Sema4a
Ensembl Gene ENSMUSG00000028064
Gene Name sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A
Synonyms SemB, SemB, Semab
Accession Numbers
Essential gene? Probably essential (E-score: 0.902) question?
Stock # IGL02076
Quality Score
Status
Chromosome 3
Chromosomal Location 88343266-88368489 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 88357829 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 225 (R225H)
Ref Sequence ENSEMBL: ENSMUSP00000118706 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029700] [ENSMUST00000107531] [ENSMUST00000123753] [ENSMUST00000125526] [ENSMUST00000127436] [ENSMUST00000169222] [ENSMUST00000166237] [ENSMUST00000165898] [ENSMUST00000184487] [ENSMUST00000185137] [ENSMUST00000141471] [ENSMUST00000147200] [ENSMUST00000184876]
AlphaFold Q62178
Predicted Effect probably damaging
Transcript: ENSMUST00000029700
AA Change: R225H

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: R225H

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Sema 64 478 1.96e-166 SMART
PSI 496 547 9.33e-13 SMART
transmembrane domain 680 702 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000107531
AA Change: R93H

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: R93H

DomainStartEndE-ValueType
Sema 2 346 2.06e-101 SMART
PSI 364 415 9.33e-13 SMART
transmembrane domain 548 570 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123753
Predicted Effect probably benign
Transcript: ENSMUST00000125526
SMART Domains Protein: ENSMUSP00000119028
Gene: ENSMUSG00000028064

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Pfam:Sema 64 113 8.2e-9 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000127436
AA Change: R225H

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064
AA Change: R225H

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Pfam:Sema 64 234 5.5e-53 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135539
Predicted Effect probably damaging
Transcript: ENSMUST00000169222
AA Change: R225H

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: R225H

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Sema 64 478 1.96e-166 SMART
PSI 496 547 9.33e-13 SMART
transmembrane domain 680 702 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000166237
AA Change: R225H

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: R225H

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Sema 64 478 1.96e-166 SMART
PSI 496 547 9.33e-13 SMART
transmembrane domain 680 702 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000165898
AA Change: R225H

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: R225H

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Sema 64 478 1.96e-166 SMART
PSI 496 547 9.33e-13 SMART
transmembrane domain 680 702 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135732
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149145
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184972
Predicted Effect probably benign
Transcript: ENSMUST00000184487
SMART Domains Protein: ENSMUSP00000139126
Gene: ENSMUSG00000028064

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Pfam:Sema 64 168 1.5e-30 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000185137
Predicted Effect probably benign
Transcript: ENSMUST00000141471
SMART Domains Protein: ENSMUSP00000114330
Gene: ENSMUSG00000028064

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000147200
SMART Domains Protein: ENSMUSP00000123061
Gene: ENSMUSG00000028064

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Pfam:Sema 64 203 3.5e-45 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000184876
SMART Domains Protein: ENSMUSP00000139159
Gene: ENSMUSG00000028064

DomainStartEndE-ValueType
signal peptide 1 32 N/A INTRINSIC
Pfam:Sema 64 179 7.7e-31 PFAM
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 encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a knock-out allele show no obvious brain defects but exhibit impaired T cell priming and defective Th1 responses. Homozygotes for a gene trap allele show severe retinal degeneration with reduced retinal vessels, depigmentation and dysfunction of both rod and cone photoreceptors. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 25 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam22 T C 5: 8,186,900 (GRCm39) Y407C probably damaging Het
Capn5 T A 7: 97,780,950 (GRCm39) K276* probably null Het
Cct4 T C 11: 22,952,394 (GRCm39) V495A probably damaging Het
Dapk3 A G 10: 81,026,131 (GRCm39) K141E probably damaging Het
Dnah2 T C 11: 69,313,385 (GRCm39) N4264S probably damaging Het
Dok1 A G 6: 83,009,812 (GRCm39) L99P probably damaging Het
Ebf3 A G 7: 136,833,030 (GRCm39) V215A possibly damaging Het
Efnb2 A G 8: 8,710,488 (GRCm39) S43P probably benign Het
Jhy G A 9: 40,828,674 (GRCm39) Q411* probably null Het
Krt73 G A 15: 101,708,370 (GRCm39) T229I probably damaging Het
Mroh8 A G 2: 157,113,882 (GRCm39) probably null Het
Olfm1 A G 2: 28,112,637 (GRCm39) T223A probably damaging Het
Oprk1 T A 1: 5,672,512 (GRCm39) D216E probably damaging Het
Or4b1d T A 2: 89,969,159 (GRCm39) E108V probably damaging Het
Or8g23 A G 9: 38,971,881 (GRCm39) L27P probably damaging Het
Pim1 T A 17: 29,712,777 (GRCm39) I230N probably damaging Het
Ppm1f A C 16: 16,732,035 (GRCm39) T162P possibly damaging Het
Rbbp8 T C 18: 11,838,876 (GRCm39) Y186H probably damaging Het
Slc15a2 A C 16: 36,582,743 (GRCm39) F215C probably damaging Het
Slc25a1 A G 16: 17,745,490 (GRCm39) C41R possibly damaging Het
Stil C A 4: 114,880,834 (GRCm39) H459Q probably benign Het
Tbc1d32 A G 10: 55,964,499 (GRCm39) I900T possibly damaging Het
Tmem33 T C 5: 67,443,446 (GRCm39) F208L probably damaging Het
Utp25 T C 1: 192,812,367 (GRCm39) H31R probably damaging Het
Vmn2r72 A G 7: 85,387,575 (GRCm39) V663A probably damaging Het
Other mutations in Sema4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00913:Sema4a APN 3 88,357,117 (GRCm39) missense probably damaging 1.00
IGL01722:Sema4a APN 3 88,345,491 (GRCm39) missense probably benign 0.14
IGL01769:Sema4a APN 3 88,357,063 (GRCm39) missense possibly damaging 0.86
IGL02202:Sema4a APN 3 88,357,050 (GRCm39) missense probably damaging 1.00
R0145:Sema4a UTSW 3 88,358,729 (GRCm39) missense probably damaging 1.00
R0386:Sema4a UTSW 3 88,344,107 (GRCm39) missense possibly damaging 0.75
R0837:Sema4a UTSW 3 88,360,405 (GRCm39) missense possibly damaging 0.46
R0863:Sema4a UTSW 3 88,355,456 (GRCm39) unclassified probably benign
R1567:Sema4a UTSW 3 88,359,353 (GRCm39) missense probably damaging 1.00
R1675:Sema4a UTSW 3 88,362,073 (GRCm39) missense possibly damaging 0.66
R1739:Sema4a UTSW 3 88,344,145 (GRCm39) missense possibly damaging 0.94
R1801:Sema4a UTSW 3 88,344,056 (GRCm39) missense probably benign 0.04
R1961:Sema4a UTSW 3 88,345,483 (GRCm39) splice site probably benign
R2029:Sema4a UTSW 3 88,358,668 (GRCm39) missense probably damaging 1.00
R4934:Sema4a UTSW 3 88,345,568 (GRCm39) missense probably damaging 1.00
R5006:Sema4a UTSW 3 88,344,091 (GRCm39) missense probably benign
R5309:Sema4a UTSW 3 88,344,343 (GRCm39) missense probably damaging 1.00
R5312:Sema4a UTSW 3 88,344,343 (GRCm39) missense probably damaging 1.00
R5338:Sema4a UTSW 3 88,358,804 (GRCm39) missense probably benign 0.01
R5481:Sema4a UTSW 3 88,360,347 (GRCm39) nonsense probably null
R5510:Sema4a UTSW 3 88,357,293 (GRCm39) critical splice donor site probably null
R6046:Sema4a UTSW 3 88,348,008 (GRCm39) missense probably damaging 1.00
R7242:Sema4a UTSW 3 88,357,416 (GRCm39) missense probably damaging 1.00
R8403:Sema4a UTSW 3 88,359,341 (GRCm39) missense probably damaging 0.98
R8798:Sema4a UTSW 3 88,344,004 (GRCm39) missense possibly damaging 0.76
R9328:Sema4a UTSW 3 88,345,613 (GRCm39) nonsense probably null
R9638:Sema4a UTSW 3 88,357,066 (GRCm39) missense probably damaging 1.00
R9728:Sema4a UTSW 3 88,348,187 (GRCm39) critical splice acceptor site probably null
Z1176:Sema4a UTSW 3 88,344,500 (GRCm39) missense probably damaging 0.97
Posted On 2014-05-07