Incidental Mutation 'R8900:Sema6a'
ID 679938
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 068757-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8900 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 47424182 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Alanine at position 242 (E242A)
Ref Sequence ENSEMBL: ENSMUSP00000121442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000126684] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect probably damaging
Transcript: ENSMUST00000019791
AA Change: E242A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: E242A

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: E242A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: E242A

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: E242A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: E242A

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: ENSMUST00000126684
SMART Domains Protein: ENSMUSP00000118655
Gene: ENSMUSG00000019647

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
Pfam:Sema 56 216 2.5e-51 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000135790
AA Change: E242A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: E242A

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: E242A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: E242A

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.4%
Validation Efficiency 100% (63/63)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca9 T C 11: 110,045,218 (GRCm39) T372A probably benign Het
Adamts8 C A 9: 30,865,930 (GRCm39) R493S probably benign Het
Ankrd33b G A 15: 31,297,830 (GRCm39) T309I probably damaging Het
Arhgap22 G A 14: 32,993,880 (GRCm39) W58* probably null Het
B4galt4 C T 16: 38,572,404 (GRCm39) probably benign Het
Bcl2a1a A T 9: 88,839,311 (GRCm39) I70L probably benign Het
Bst1 A G 5: 43,977,942 (GRCm39) D97G possibly damaging Het
Cand2 C T 6: 115,757,894 (GRCm39) T52M probably benign Het
Cd101 C A 3: 100,926,062 (GRCm39) R219L probably benign Het
Cd5l T A 3: 87,274,882 (GRCm39) D140E probably benign Het
Cdcp3 A T 7: 130,904,197 (GRCm39) probably benign Het
Cebpa A G 7: 34,819,906 (GRCm39) M355V possibly damaging Het
Cfap74 G A 4: 155,521,187 (GRCm39) E620K Het
Clec4a4 A G 6: 123,000,875 (GRCm39) E196G probably damaging Het
Cpxm1 T A 2: 130,235,360 (GRCm39) D544V probably damaging Het
Cwf19l2 T A 9: 3,447,245 (GRCm39) D535E probably benign Het
Daw1 T G 1: 83,175,898 (GRCm39) L212R probably benign Het
Dnm3 T A 1: 162,135,445 (GRCm39) T443S probably benign Het
Dock9 T C 14: 121,817,940 (GRCm39) D1627G probably damaging Het
Dohh A G 10: 81,223,735 (GRCm39) I263V probably benign Het
Dsp G A 13: 38,365,155 (GRCm39) V513M probably damaging Het
Dus4l G T 12: 31,690,692 (GRCm39) L320I possibly damaging Het
Edc4 A C 8: 106,617,857 (GRCm39) Q1139P probably damaging Het
Fam220a T A 5: 143,549,228 (GRCm39) C213* probably null Het
Fgf14 A T 14: 124,221,326 (GRCm39) Y159* probably null Het
Gm45861 A T 8: 28,019,632 (GRCm39) D749V unknown Het
Hip1 T C 5: 135,459,144 (GRCm39) T203A probably benign Het
Igfals A G 17: 25,099,014 (GRCm39) D35G possibly damaging Het
Itga4 T A 2: 79,145,332 (GRCm39) I716K probably damaging Het
Ncaph2 T A 15: 89,253,594 (GRCm39) I282N probably benign Het
Ndufb3 T C 1: 58,634,824 (GRCm39) Y59H probably damaging Het
Nxpe3 T C 16: 55,665,023 (GRCm39) H399R probably damaging Het
Nxph1 T C 6: 9,247,601 (GRCm39) S191P probably damaging Het
Or13c7e-ps1 G T 4: 43,781,432 (GRCm39) S299R probably benign Het
Or1p1 T C 11: 74,180,413 (GRCm39) S314P probably damaging Het
Pcdha11 T G 18: 37,145,799 (GRCm39) I630S probably damaging Het
Pfkl C G 10: 77,836,615 (GRCm39) G134A probably damaging Het
Phf19 A T 2: 34,795,484 (GRCm39) C196S probably damaging Het
Piezo2 T C 18: 63,248,096 (GRCm39) K468R probably benign Het
Plekhn1 T C 4: 156,310,078 (GRCm39) S79G possibly damaging Het
Pomk A G 8: 26,473,384 (GRCm39) Y190H possibly damaging Het
Ppp1r13b T A 12: 111,838,778 (GRCm39) E33D probably damaging Het
Raly A T 2: 154,705,493 (GRCm39) I174F probably damaging Het
Rint1 T C 5: 24,016,882 (GRCm39) V549A possibly damaging Het
Rnf31 T G 14: 55,833,689 (GRCm39) C566G probably damaging Het
Scart1 G A 7: 139,808,478 (GRCm39) W796* probably null Het
Sdc1 C T 12: 8,840,460 (GRCm39) T79I possibly damaging Het
Slc22a30 A C 19: 8,315,340 (GRCm39) M430R probably damaging Het
Sp9 C A 2: 73,103,863 (GRCm39) T139K probably benign Het
Tbkbp1 T C 11: 97,040,327 (GRCm39) D29G probably benign Het
Tcf4 T C 18: 69,697,761 (GRCm39) probably benign Het
Tenm3 A T 8: 48,689,437 (GRCm39) I2050N probably damaging Het
Tiparp T A 3: 65,460,603 (GRCm39) F531I probably damaging Het
Tmem132b A T 5: 125,855,884 (GRCm39) I539F probably damaging Het
Ttf2 T C 3: 100,859,956 (GRCm39) D666G probably damaging Het
Vmn1r51 T C 6: 90,106,842 (GRCm39) S253P probably damaging Het
Vmn2r104 A G 17: 20,261,924 (GRCm39) I402T probably damaging Het
Vmn2r16 T C 5: 109,511,619 (GRCm39) Y609H probably benign Het
Vmn2r17 A T 5: 109,575,863 (GRCm39) M245L probably benign Het
Vmn2r42 C T 7: 8,197,792 (GRCm39) E276K probably benign Het
Wdr75 C A 1: 45,838,287 (GRCm39) N65K probably damaging Het
Zbtb47 A C 9: 121,596,705 (GRCm39) K687T probably damaging Het
Zfhx4 T C 3: 5,463,924 (GRCm39) S1361P probably damaging Het
Zfp317 T A 9: 19,558,708 (GRCm39) C396* probably null 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
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
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'- TCAGGTTTCCAGACAGCTTAGTC -3'
(R):5'- TAGCGCTTGCACTTCTGAAGTC -3'

Sequencing Primer
(F):5'- AGACAGCTTAGTCTGTCACTTCTGG -3'
(R):5'- GTGTTAACCACATGTCTAATAGCCC -3'
Posted On 2021-08-31