Incidental Mutation 'R0557:Sema6a'
ID 45683
Institutional Source Beutler Lab
Gene Symbol Sema6a
Ensembl Gene ENSMUSG00000019647
Gene Name sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
Synonyms VIa, Semaq, Sema6A-1, sema, A730020P05Rik
MMRRC Submission 038749-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0557 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 47382567 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 660 (V660A)
Ref Sequence ENSEMBL: ENSMUSP00000121442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect probably benign
Transcript: ENSMUST00000019791
AA Change: V660A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: V660A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Sema 56 487 1.06e-185 SMART
PSI 514 569 9.57e-1 SMART
transmembrane domain 648 670 N/A INTRINSIC
low complexity region 932 951 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000076043
AA Change: V605A

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: V605A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Sema 56 487 1.06e-185 SMART
PSI 514 569 9.57e-1 SMART
transmembrane domain 593 615 N/A INTRINSIC
low complexity region 877 896 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000115449
AA Change: V634A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: V634A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Sema 56 461 1.24e-168 SMART
PSI 488 543 9.57e-1 SMART
transmembrane domain 622 644 N/A INTRINSIC
low complexity region 906 925 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123228
SMART Domains Protein: ENSMUSP00000120249
Gene: ENSMUSG00000019647

DomainStartEndE-ValueType
Blast:PSI 2 45 4e-26 BLAST
PDB:3OKY|B 2 47 2e-26 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000135790
AA Change: V677A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: V677A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Sema 56 487 1.06e-185 SMART
PSI 514 569 9.57e-1 SMART
transmembrane domain 665 687 N/A INTRINSIC
low complexity region 949 968 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000156422
AA Change: V660A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: V660A

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Sema 56 487 1.06e-185 SMART
PSI 514 569 9.57e-1 SMART
transmembrane domain 648 670 N/A INTRINSIC
low complexity region 932 951 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection (Leighton et al., 2001 [PubMed 11242070]).[supplied by OMIM, Feb 2011]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit defects in lamina-specific neurite stratification of specific retinal neuron subtypes and disruption of the dendritic plexus organization of On but not Off starburst amacrine cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610008E11Rik G A 10: 78,903,519 (GRCm39) H266Y probably damaging Het
Abi3bp C T 16: 56,488,750 (GRCm39) R1294C probably damaging Het
Acot3 T C 12: 84,105,630 (GRCm39) Y366H probably damaging Het
Ago1 A G 4: 126,353,817 (GRCm39) V254A probably benign Het
Ahnak T A 19: 8,979,308 (GRCm39) D197E probably benign Het
Aldh1b1 A T 4: 45,802,647 (GRCm39) T62S probably benign Het
Alox12e T C 11: 70,212,274 (GRCm39) R135G possibly damaging Het
Amn1 T C 6: 149,072,503 (GRCm39) Y78C possibly damaging Het
Ankmy2 G A 12: 36,237,765 (GRCm39) S288N probably benign Het
Ano3 A T 2: 110,693,297 (GRCm39) probably null Het
Arfgap3 T C 15: 83,187,386 (GRCm39) D491G probably damaging Het
Arhgap15 T C 2: 44,006,629 (GRCm39) S249P possibly damaging Het
Atp9b A G 18: 80,809,137 (GRCm39) V211A probably damaging Het
Cabin1 A G 10: 75,562,751 (GRCm39) Y12H probably damaging Het
Cdkn2aip T C 8: 48,165,977 (GRCm39) T110A probably damaging Het
Cemip2 C T 19: 21,789,267 (GRCm39) A567V probably benign Het
Chchd6 A G 6: 89,551,569 (GRCm39) S31P probably damaging Het
Chrna3 A G 9: 54,923,149 (GRCm39) Y220H probably damaging Het
Ctu1 A G 7: 43,326,583 (GRCm39) D414G unknown Het
Cxxc1 C T 18: 74,351,845 (GRCm39) R241W possibly damaging Het
Cyp3a16 A G 5: 145,406,398 (GRCm39) I18T unknown Het
Dip2c A T 13: 9,603,495 (GRCm39) I405F possibly damaging Het
Disp3 A T 4: 148,325,861 (GRCm39) M1299K possibly damaging Het
Dnah9 T G 11: 65,975,492 (GRCm39) H1519P probably damaging Het
Ehd3 C A 17: 74,136,928 (GRCm39) Q366K probably benign Het
Exosc3 A T 4: 45,316,957 (GRCm39) M232K probably damaging Het
Fancm T C 12: 65,165,216 (GRCm39) probably null Het
Fgfr2 A G 7: 129,820,811 (GRCm39) V241A probably damaging Het
Gdf2 C T 14: 33,663,178 (GRCm39) P24L probably damaging Het
Hars2 T C 18: 36,924,130 (GRCm39) I489T possibly damaging Het
Ice1 T C 13: 70,749,310 (GRCm39) I1945V probably benign Het
Il33 A C 19: 29,932,036 (GRCm39) N143T probably damaging Het
Ilvbl G A 10: 78,419,321 (GRCm39) W313* probably null Het
Insyn2a A G 7: 134,520,434 (GRCm39) L32P probably damaging Het
Isca1 G T 13: 59,904,788 (GRCm39) Q91K possibly damaging Het
Kcnh5 T A 12: 75,161,323 (GRCm39) Y195F probably damaging Het
Lama4 T G 10: 38,964,393 (GRCm39) I1355S probably benign Het
Lonrf1 T C 8: 36,697,574 (GRCm39) D470G probably benign Het
Mak A G 13: 41,193,135 (GRCm39) Y446H probably benign Het
Mki67 C T 7: 135,300,990 (GRCm39) S1348N possibly damaging Het
Mpzl3 A G 9: 44,977,806 (GRCm39) Y138C probably damaging Het
Myh8 T C 11: 67,192,624 (GRCm39) L1501P possibly damaging Het
Naa35 A G 13: 59,775,778 (GRCm39) E552G probably damaging Het
Ncor2 A T 5: 125,183,369 (GRCm39) L200* probably null Het
Nrm T C 17: 36,175,524 (GRCm39) V210A probably damaging Het
Nt5e T A 9: 88,248,519 (GRCm39) N405K probably damaging Het
Or1j4 T A 2: 36,740,760 (GRCm39) I234N possibly damaging Het
Or1o11 T A 17: 37,756,712 (GRCm39) I100N probably damaging Het
Orc2 T C 1: 58,508,846 (GRCm39) S434G probably damaging Het
Plcb4 G A 2: 135,796,269 (GRCm39) V388I probably damaging Het
Ppm1l A G 3: 69,405,234 (GRCm39) D177G probably benign Het
Prl8a2 A T 13: 27,536,875 (GRCm39) R165* probably null Het
Ptbp3 G A 4: 59,517,684 (GRCm39) R66* probably null Het
Pten A G 19: 32,795,290 (GRCm39) T286A probably benign Het
Rac2 C T 15: 78,449,174 (GRCm39) V113M probably damaging Het
Rai1 C T 11: 60,081,321 (GRCm39) T1795I probably benign Het
Ros1 T G 10: 51,961,359 (GRCm39) K1792Q possibly damaging Het
Slc22a23 C T 13: 34,528,366 (GRCm39) G139S possibly damaging Het
Slc26a5 A G 5: 22,024,762 (GRCm39) S441P probably damaging Het
Slc27a3 A G 3: 90,294,163 (GRCm39) L462P probably damaging Het
Spag5 T A 11: 78,205,037 (GRCm39) S607R probably damaging Het
Spata18 A T 5: 73,809,013 (GRCm39) N29Y probably damaging Het
Spata20 C T 11: 94,376,048 (GRCm39) R22H probably benign Het
Spsb2 A C 6: 124,787,355 (GRCm39) Y263S probably damaging Het
Sptbn4 C A 7: 27,107,753 (GRCm39) E885* probably null Het
Syne2 T C 12: 75,976,075 (GRCm39) I1175T probably benign Het
Tmem209 A C 6: 30,501,913 (GRCm39) H253Q probably damaging Het
Trip12 A T 1: 84,702,468 (GRCm39) D788E probably damaging Het
Usp34 T C 11: 23,353,848 (GRCm39) S1509P probably damaging Het
Utp20 A T 10: 88,584,173 (GRCm39) D2661E probably damaging Het
Vars1 C A 17: 35,223,960 (GRCm39) P264Q possibly damaging Het
Vmn2r66 T G 7: 84,643,972 (GRCm39) S813R probably damaging Het
Wipf2 C A 11: 98,782,915 (GRCm39) Q114K possibly damaging Het
Wnt5b G T 6: 119,410,779 (GRCm39) H220Q probably damaging Het
Xirp2 A G 2: 67,346,695 (GRCm39) T2979A probably benign Het
Zfyve9 A G 4: 108,531,708 (GRCm39) V408A probably damaging Het
Zzef1 T C 11: 72,808,556 (GRCm39) S2744P probably damaging Het
Other mutations in Sema6a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Sema6a APN 18 47,423,042 (GRCm39) critical splice donor site probably null
IGL01351:Sema6a APN 18 47,414,369 (GRCm39) missense possibly damaging 0.84
IGL01594:Sema6a APN 18 47,381,884 (GRCm39) missense probably damaging 1.00
IGL01953:Sema6a APN 18 47,423,187 (GRCm39) nonsense probably null
IGL02077:Sema6a APN 18 47,416,465 (GRCm39) missense possibly damaging 0.94
IGL02632:Sema6a APN 18 47,423,222 (GRCm39) missense probably damaging 1.00
IGL02957:Sema6a APN 18 47,382,291 (GRCm39) missense probably damaging 1.00
IGL03013:Sema6a APN 18 47,381,461 (GRCm39) missense probably benign 0.01
IGL03279:Sema6a APN 18 47,433,157 (GRCm39) nonsense probably null
saphire UTSW 18 47,439,496 (GRCm39) nonsense probably null
IGL02988:Sema6a UTSW 18 47,431,281 (GRCm39) missense probably damaging 1.00
R0114:Sema6a UTSW 18 47,423,244 (GRCm39) missense probably damaging 1.00
R0311:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0312:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0347:Sema6a UTSW 18 47,424,196 (GRCm39) missense probably damaging 1.00
R0350:Sema6a UTSW 18 47,403,785 (GRCm39) missense probably benign
R0366:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0368:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0391:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0403:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0466:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0515:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0517:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0542:Sema6a UTSW 18 47,381,643 (GRCm39) missense probably damaging 1.00
R0569:Sema6a UTSW 18 47,403,872 (GRCm39) splice site probably null
R0650:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0689:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0694:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0726:Sema6a UTSW 18 47,425,048 (GRCm39) missense probably damaging 1.00
R0741:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0821:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0824:Sema6a UTSW 18 47,423,112 (GRCm39) splice site probably null
R0924:Sema6a UTSW 18 47,381,559 (GRCm39) missense probably damaging 1.00
R1108:Sema6a UTSW 18 47,439,498 (GRCm39) missense probably benign 0.02
R1255:Sema6a UTSW 18 47,382,366 (GRCm39) missense probably damaging 0.98
R1422:Sema6a UTSW 18 47,439,498 (GRCm39) missense probably benign 0.02
R1531:Sema6a UTSW 18 47,382,066 (GRCm39) missense probably damaging 1.00
R1707:Sema6a UTSW 18 47,416,512 (GRCm39) missense probably benign 0.04
R1746:Sema6a UTSW 18 47,439,416 (GRCm39) splice site probably benign
R1807:Sema6a UTSW 18 47,409,491 (GRCm39) missense possibly damaging 0.85
R1974:Sema6a UTSW 18 47,403,696 (GRCm39) missense probably benign 0.04
R1987:Sema6a UTSW 18 47,433,209 (GRCm39) missense probably damaging 1.00
R2044:Sema6a UTSW 18 47,439,496 (GRCm39) nonsense probably null
R3719:Sema6a UTSW 18 47,382,144 (GRCm39) missense probably damaging 1.00
R4491:Sema6a UTSW 18 47,439,524 (GRCm39) utr 5 prime probably benign
R4552:Sema6a UTSW 18 47,424,990 (GRCm39) missense probably damaging 1.00
R4707:Sema6a UTSW 18 47,381,779 (GRCm39) missense probably benign 0.43
R4710:Sema6a UTSW 18 47,403,750 (GRCm39) missense probably benign 0.00
R4713:Sema6a UTSW 18 47,382,363 (GRCm39) missense possibly damaging 0.79
R4963:Sema6a UTSW 18 47,431,318 (GRCm39) missense possibly damaging 0.48
R5088:Sema6a UTSW 18 47,382,196 (GRCm39) missense probably damaging 1.00
R5133:Sema6a UTSW 18 47,433,195 (GRCm39) missense probably damaging 1.00
R5135:Sema6a UTSW 18 47,424,239 (GRCm39) missense probably damaging 1.00
R5141:Sema6a UTSW 18 47,381,455 (GRCm39) missense probably damaging 1.00
R5277:Sema6a UTSW 18 47,409,611 (GRCm39) intron probably benign
R5551:Sema6a UTSW 18 47,381,595 (GRCm39) missense possibly damaging 0.76
R5618:Sema6a UTSW 18 47,415,015 (GRCm39) missense probably damaging 0.98
R5717:Sema6a UTSW 18 47,382,330 (GRCm39) missense probably benign 0.01
R5729:Sema6a UTSW 18 47,414,410 (GRCm39) missense probably damaging 1.00
R5779:Sema6a UTSW 18 47,381,893 (GRCm39) missense probably damaging 1.00
R5917:Sema6a UTSW 18 47,414,405 (GRCm39) missense probably benign 0.05
R6054:Sema6a UTSW 18 47,416,470 (GRCm39) missense possibly damaging 0.94
R6142:Sema6a UTSW 18 47,414,266 (GRCm39) missense probably benign 0.00
R6209:Sema6a UTSW 18 47,431,369 (GRCm39) splice site probably null
R6307:Sema6a UTSW 18 47,382,231 (GRCm39) missense probably damaging 1.00
R6734:Sema6a UTSW 18 47,412,236 (GRCm39) missense probably benign 0.31
R7014:Sema6a UTSW 18 47,431,284 (GRCm39) missense probably damaging 1.00
R7033:Sema6a UTSW 18 47,381,637 (GRCm39) missense probably damaging 0.96
R7574:Sema6a UTSW 18 47,424,231 (GRCm39) missense probably damaging 1.00
R8054:Sema6a UTSW 18 47,424,972 (GRCm39) missense probably damaging 1.00
R8250:Sema6a UTSW 18 47,423,182 (GRCm39) missense probably damaging 0.99
R8408:Sema6a UTSW 18 47,381,958 (GRCm39) missense probably benign 0.34
R8411:Sema6a UTSW 18 47,382,022 (GRCm39) missense probably benign 0.00
R8900:Sema6a UTSW 18 47,424,182 (GRCm39) missense probably damaging 1.00
R9140:Sema6a UTSW 18 47,415,009 (GRCm39) missense probably benign
R9158:Sema6a UTSW 18 47,431,330 (GRCm39) missense probably damaging 0.98
R9488:Sema6a UTSW 18 47,437,216 (GRCm39) missense probably damaging 1.00
R9565:Sema6a UTSW 18 47,382,594 (GRCm39) missense probably null 1.00
R9652:Sema6a UTSW 18 47,382,252 (GRCm39) missense probably damaging 1.00
R9732:Sema6a UTSW 18 47,381,925 (GRCm39) missense probably damaging 0.96
X0065:Sema6a UTSW 18 47,416,386 (GRCm39) missense possibly damaging 0.78
Predicted Primers PCR Primer
(F):5'- AGCCTTGATGAGCATCTTGGCG -3'
(R):5'- GCCCTGAAGATGAGCTATGCAGAG -3'

Sequencing Primer
(F):5'- AGGATGGCCTCAGGCTTTG -3'
(R):5'- TGCAGAGGTGCTATCATCAC -3'
Posted On 2013-06-11