Incidental Mutation 'R0924:Sema6a'
ID 83123
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 039071-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0924 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 47381559 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 996 (L996P)
Ref Sequence ENSEMBL: ENSMUSP00000121442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect probably damaging
Transcript: ENSMUST00000019791
AA Change: L996P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: L996P

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 damaging
Transcript: ENSMUST00000076043
AA Change: L941P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: L941P

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 damaging
Transcript: ENSMUST00000115449
AA Change: L970P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: L970P

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 damaging
Transcript: ENSMUST00000135790
AA Change: L1013P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: L1013P

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 damaging
Transcript: ENSMUST00000156422
AA Change: L996P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: L996P

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
Meta Mutation Damage Score 0.2074 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.9%
  • 10x: 97.7%
  • 20x: 96.2%
Validation Efficiency 97% (69/71)
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts18 A T 8: 114,432,028 (GRCm39) probably null Het
Ahcyl2 A C 6: 29,870,627 (GRCm39) probably null Het
Ajap1 T A 4: 153,470,929 (GRCm39) I293F probably damaging Het
Akap10 T C 11: 61,795,689 (GRCm39) probably benign Het
Aldh3b2 T C 19: 4,029,350 (GRCm39) V241A probably benign Het
Anxa6 A T 11: 54,885,214 (GRCm39) probably null Het
Atpaf1 T A 4: 115,652,635 (GRCm39) V12D probably damaging Het
Aurkb C A 11: 68,936,822 (GRCm39) Y12* probably null Het
Bicdl1 A G 5: 115,799,587 (GRCm39) probably benign Het
Bnc1 A T 7: 81,628,156 (GRCm39) probably benign Het
Bpi A G 2: 158,103,346 (GRCm39) I114V possibly damaging Het
Cacna1c A T 6: 118,652,857 (GRCm39) I772N probably damaging Het
Cacna2d1 A G 5: 16,570,860 (GRCm39) N1045D possibly damaging Het
Ccrl2 A G 9: 110,885,036 (GRCm39) V154A probably benign Het
Celsr3 C A 9: 108,723,224 (GRCm39) Q2831K possibly damaging Het
Cplane1 T C 15: 8,280,554 (GRCm39) probably benign Het
Cul3 A T 1: 80,267,835 (GRCm39) M102K probably damaging Het
Cwf19l2 T C 9: 3,441,047 (GRCm39) probably benign Het
Dlg5 G A 14: 24,185,645 (GRCm39) P1920L probably damaging Het
Dnah2 T C 11: 69,312,134 (GRCm39) H4393R probably damaging Het
Eif2b3 T A 4: 116,938,775 (GRCm39) V408D possibly damaging Het
Eml3 T C 19: 8,910,675 (GRCm39) probably null Het
Enpp2 T C 15: 54,770,355 (GRCm39) probably benign Het
Fcgbpl1 A T 7: 27,839,555 (GRCm39) Y456F probably damaging Het
Gm14178 T A 11: 99,638,326 (GRCm39) T18S Het
H2bc12 G A 13: 22,220,210 (GRCm39) D52N probably damaging Het
H2-M11 A G 17: 36,860,106 (GRCm39) M324V probably benign Het
H2-T13 A T 17: 36,394,824 (GRCm39) V33E probably damaging Het
Hdac10 T C 15: 89,010,065 (GRCm39) T298A probably benign Het
Hepacam A C 9: 37,295,224 (GRCm39) probably benign Het
Hmx3 A T 7: 131,144,813 (GRCm39) H41L probably benign Het
Ifi27l2a A G 12: 103,408,639 (GRCm39) V68A probably damaging Het
Itga11 A G 9: 62,683,956 (GRCm39) E1079G probably benign Het
Krt6a T C 15: 101,599,235 (GRCm39) probably benign Het
L1td1 A G 4: 98,625,862 (GRCm39) N686D probably damaging Het
Lrrtm2 G A 18: 35,346,808 (GRCm39) R165C probably damaging Het
Macf1 G T 4: 123,279,271 (GRCm39) A3910E probably damaging Het
Muc5ac A T 7: 141,361,252 (GRCm39) Y1521F possibly damaging Het
Myo7a A T 7: 97,747,463 (GRCm39) I129N probably damaging Het
Ncam1 A T 9: 49,473,476 (GRCm39) probably benign Het
Nckap1 A T 2: 80,384,593 (GRCm39) C114S probably benign Het
Nf1 T G 11: 79,344,692 (GRCm39) W1260G probably damaging Het
Or3a1d T C 11: 74,237,624 (GRCm39) Y262C probably damaging Het
Or6b2b A G 1: 92,419,127 (GRCm39) S117P possibly damaging Het
Or6c76b A T 10: 129,692,515 (GRCm39) I43F probably damaging Het
Oxtr A T 6: 112,466,598 (GRCm39) probably null Het
Pabpc4 C T 4: 123,188,458 (GRCm39) R356C possibly damaging Het
Pcbp2 T A 15: 102,398,197 (GRCm39) D182E probably damaging Het
Pgm2 A T 5: 64,269,490 (GRCm39) I526F possibly damaging Het
Rab43 A T 6: 87,769,752 (GRCm39) Y151* probably null Het
Rbm19 A G 5: 120,264,269 (GRCm39) E343G probably benign Het
Rel A T 11: 23,692,439 (GRCm39) D531E probably benign Het
Rfx4 T A 10: 84,704,291 (GRCm39) V262E probably damaging Het
Rnf31 T C 14: 55,830,459 (GRCm39) probably benign Het
Robo3 T A 9: 37,340,778 (GRCm39) probably benign Het
Ryr3 A G 2: 112,672,178 (GRCm39) L1431P probably damaging Het
Sema3d A C 5: 12,513,183 (GRCm39) D51A possibly damaging Het
Sh2d4a T A 8: 68,787,775 (GRCm39) F294I probably damaging Het
Sorl1 T A 9: 41,919,470 (GRCm39) probably benign Het
Sox1ot G T 8: 12,480,455 (GRCm39) noncoding transcript Het
Spsb3 A T 17: 25,110,358 (GRCm39) N395I probably damaging Het
Sptan1 A G 2: 29,906,040 (GRCm39) N1662S probably damaging Het
Srd5a2 G T 17: 74,331,516 (GRCm39) N160K probably damaging Het
Sting1 A G 18: 35,868,154 (GRCm39) probably null Het
Tmem132d G A 5: 128,061,503 (GRCm39) probably benign Het
Unc80 A T 1: 66,549,800 (GRCm39) Q686L possibly damaging Het
Vmn2r93 A G 17: 18,524,443 (GRCm39) T146A probably benign Het
Wdr19 A G 5: 65,413,782 (GRCm39) probably benign Het
Zfp646 C T 7: 127,482,982 (GRCm39) Q1500* probably null Het
Zfp683 T C 4: 133,783,138 (GRCm39) Y201H probably benign 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
R0557:Sema6a UTSW 18 47,382,567 (GRCm39) missense probably benign 0.01
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
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'- ATCGGATGCTTCAACTCCTGGC -3'
(R):5'- GTGAACCTTGTGGAGAACCTGGAC -3'

Sequencing Primer
(F):5'- TCAACTCCTGGCCCCCC -3'
(R):5'- TAAAGTTCCACAGCGCGAG -3'
Posted On 2013-11-08