Incidental Mutation 'R9140:Sema6a'
ID 694319
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 068972-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9140 (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 C at 47415009 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 427 (N427S)
Ref Sequence ENSEMBL: ENSMUSP00000019791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
PDB Structure Mouse Semaphorin 6A extracellular domain [X-RAY DIFFRACTION]
Plexin A2 / Semaphorin 6A complex [X-RAY DIFFRACTION]
Mouse Semaphorin 6A, extracellular domains 1-2 [X-RAY DIFFRACTION]
Plexin A2 in complex with Semaphorin 6A [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000019791
AA Change: N427S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: N427S

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: N427S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: N427S

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: N427S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: N427S

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: N427S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: N427S

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: N427S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: N427S

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 0.0846 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (69/69)
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
Actl9 A T 17: 33,652,170 (GRCm39) I77F possibly damaging Het
Adgb G A 10: 10,216,263 (GRCm39) R1509* probably null Het
Ago1 C A 4: 126,336,977 (GRCm39) V547L probably benign Het
Arhgap21 T A 2: 20,886,025 (GRCm39) Y394F probably damaging Het
C1qa A C 4: 136,623,553 (GRCm39) I217S probably damaging Het
Cacna1b T A 2: 24,525,224 (GRCm39) I1651F probably damaging Het
Car8 T C 4: 8,183,270 (GRCm39) T242A probably benign Het
Ccdc121rt3 A T 5: 112,502,723 (GRCm39) L327Q probably damaging Het
Ccn4 G A 15: 66,791,157 (GRCm39) V320M probably damaging Het
Chrnb4 G A 9: 54,941,955 (GRCm39) H440Y Het
Cic T C 7: 24,985,165 (GRCm39) V1137A probably damaging Het
Ctdp1 C T 18: 80,484,043 (GRCm39) probably null Het
Cyp3a16 G C 5: 145,406,434 (GRCm39) A6G unknown Het
Ddhd1 A C 14: 45,894,918 (GRCm39) L184R probably benign Het
Dnttip1 A G 2: 164,596,082 (GRCm39) D109G possibly damaging Het
Dsc3 T A 18: 20,122,616 (GRCm39) M103L probably benign Het
Dusp9 TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG X: 72,684,217 (GRCm39) probably benign Het
Elapor2 T C 5: 9,449,226 (GRCm39) V118A probably benign Het
Eya2 T C 2: 165,608,977 (GRCm39) L439S probably damaging Het
Eya3 A G 4: 132,428,411 (GRCm39) N311S possibly damaging Het
Fam151a C T 4: 106,605,344 (GRCm39) R569* probably null Het
Fer1l5 A G 1: 36,460,047 (GRCm39) probably benign Het
Fnbp4 A G 2: 90,576,077 (GRCm39) T93A unknown Het
Fosl2 T C 5: 32,310,042 (GRCm39) S164P probably damaging Het
Galc T C 12: 98,173,673 (GRCm39) T630A probably null Het
Gm5916 G T 9: 36,031,982 (GRCm39) Q101K unknown Het
Gm7138 A T 10: 77,612,682 (GRCm39) probably benign Het
Habp2 A G 19: 56,307,934 (GRCm39) K474R probably benign Het
Ibtk A G 9: 85,617,114 (GRCm39) F153L probably damaging Het
Idh2 TCCCAGG T 7: 79,748,079 (GRCm39) probably benign Het
Jup C T 11: 100,270,391 (GRCm39) C372Y probably damaging Het
Kirrel3 C T 9: 34,924,596 (GRCm39) A268V probably benign Het
Kprp G T 3: 92,732,458 (GRCm39) Y197* probably null Het
Kri1 C T 9: 21,187,434 (GRCm39) R471H Het
Krt17 C A 11: 100,148,476 (GRCm39) A322S possibly damaging Het
Leng9 A T 7: 4,152,657 (GRCm39) D6E probably benign Het
Macf1 A T 4: 123,367,855 (GRCm39) I2302K possibly damaging Het
Manba G A 3: 135,191,490 (GRCm39) V17M probably benign Het
Mical2 A G 7: 112,006,826 (GRCm39) K582E probably damaging Het
Mknk2 A G 10: 80,507,427 (GRCm39) V102A probably benign Het
Myh1 G A 11: 67,100,089 (GRCm39) G636D probably benign Het
Or51q1c A G 7: 103,653,322 (GRCm39) N280S probably damaging Het
P2rx7 G A 5: 122,790,789 (GRCm39) probably null Het
Pcmt1 A G 10: 7,514,678 (GRCm39) *177R probably null Het
Pla2r1 T C 2: 60,271,455 (GRCm39) K959R probably benign Het
Plat A G 8: 23,270,562 (GRCm39) D493G probably damaging Het
Prr30 A G 14: 101,436,430 (GRCm39) L44P probably benign Het
Ptx4 T C 17: 25,344,180 (GRCm39) C477R probably damaging Het
Pus10 A G 11: 23,622,625 (GRCm39) S82G probably benign Het
Pygo1 A G 9: 72,852,988 (GRCm39) T392A probably benign Het
Rad54b C A 4: 11,610,386 (GRCm39) L668I probably damaging Het
Rdh19 A C 10: 127,692,830 (GRCm39) M166L Het
Retnlg C A 16: 48,693,288 (GRCm39) Q22K possibly damaging Het
Rfc3 G T 5: 151,568,141 (GRCm39) T249K probably benign Het
Rgs16 T A 1: 153,619,381 (GRCm39) V129E probably damaging Het
Rptn T A 3: 93,303,445 (GRCm39) Y259* probably null Het
Slc7a13 T C 4: 19,819,487 (GRCm39) I229T possibly damaging Het
Slitrk3 A T 3: 72,957,792 (GRCm39) Y327N probably benign Het
Smtnl2 A G 11: 72,290,793 (GRCm39) L384P probably damaging Het
Stil G T 4: 114,864,449 (GRCm39) V117F probably damaging Het
Tada1 T C 1: 166,216,177 (GRCm39) V126A probably benign Het
Tasor2 G A 13: 3,638,441 (GRCm39) T430I probably benign Het
Tmem30c T C 16: 57,090,482 (GRCm39) I242V probably damaging Het
Tnnt2 T A 1: 135,768,635 (GRCm39) V8E Het
Ttn A G 2: 76,774,240 (GRCm39) V2268A unknown Het
Uspl1 G T 5: 149,150,290 (GRCm39) A497S possibly damaging Het
Vmn2r1 A T 3: 63,997,465 (GRCm39) N374Y probably benign Het
Vmn2r27 A G 6: 124,169,207 (GRCm39) F641S probably damaging Het
Vmn2r52 T A 7: 9,892,643 (GRCm39) Y832F probably damaging Het
Zfp748 C T 13: 67,689,073 (GRCm39) C729Y 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
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
R8900:Sema6a UTSW 18 47,424,182 (GRCm39) missense probably damaging 1.00
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'- TTGTCTGCCAAGATTTTCCATG -3'
(R):5'- TAAGGGACCAGACCAGCTTG -3'

Sequencing Primer
(F):5'- GTCTGCCAAGATTTTCCATGAATGG -3'
(R):5'- CCAGCTTGAGAACATTACTTACATGC -3'
Posted On 2022-01-20