Incidental Mutation 'R9158:Sema6a'
ID 695540
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 068942-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9158 (G1)
Quality Score 225.009
Status Validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 47431330 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 123 (V123I)
Ref Sequence ENSEMBL: ENSMUSP00000019791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000126684] [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 damaging
Transcript: ENSMUST00000019791
AA Change: V123I

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: V123I

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: V123I

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: V123I

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: V123I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: V123I

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 damaging
Transcript: ENSMUST00000126684
AA Change: V123I

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000118655
Gene: ENSMUSG00000019647
AA Change: V123I

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: V123I

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: V123I

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: V123I

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: V123I

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: 100.0%
  • 10x: 99.8%
  • 20x: 99.5%
Validation Efficiency 100% (62/62)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam25 G A 8: 41,208,645 (GRCm39) C637Y probably damaging Het
Ahdc1 A G 4: 132,792,505 (GRCm39) T1249A possibly damaging Het
Alkbh3 A G 2: 93,835,082 (GRCm39) S88P probably damaging Het
Ankrd17 C A 5: 90,416,575 (GRCm39) A1086S probably damaging Het
Ankzf1 T A 1: 75,173,020 (GRCm39) V372E probably damaging Het
Apbb1ip T C 2: 22,764,951 (GRCm39) V544A probably benign Het
Atp13a2 T C 4: 140,724,112 (GRCm39) probably null Het
Cacna2d1 A G 5: 16,140,039 (GRCm39) T10A probably benign Het
Cadps T C 14: 12,546,356 (GRCm38) N500S probably benign Het
Casp16 A G 17: 23,769,948 (GRCm39) probably benign Het
Cdh22 T A 2: 165,012,627 (GRCm39) I153F probably damaging Het
Clip2 T C 5: 134,521,251 (GRCm39) E964G probably benign Het
Cracdl A T 1: 37,670,442 (GRCm39) M166K probably damaging Het
Cryga T C 1: 65,142,198 (GRCm39) D65G probably benign Het
Dap3 A G 3: 88,832,637 (GRCm39) Y357H probably damaging Het
Eef2 C T 10: 81,014,693 (GRCm39) probably benign Het
Gja4 A G 4: 127,206,466 (GRCm39) L99P probably damaging Het
Glb1l3 A T 9: 26,765,005 (GRCm39) Y135* probably null Het
Gm5114 T G 7: 39,060,486 (GRCm39) D121A probably damaging Het
Gm6525 A G 3: 84,082,255 (GRCm39) K59E probably benign Het
Herc1 C T 9: 66,376,400 (GRCm39) L3407F probably benign Het
Hmgcr G A 13: 96,792,170 (GRCm39) R589* probably null Het
Iglv3 A C 16: 19,060,012 (GRCm39) D105E probably damaging Het
Il1r1 G A 1: 40,332,391 (GRCm39) W60* probably null Het
Il31ra C T 13: 112,670,394 (GRCm39) W331* probably null Het
Inca1 C T 11: 70,581,376 (GRCm39) C16Y probably damaging Het
Inpp4a A G 1: 37,442,552 (GRCm39) T628A possibly damaging Het
Kdm2a C G 19: 4,374,715 (GRCm39) R805S possibly damaging Het
Kel T A 6: 41,664,905 (GRCm39) I620L probably benign Het
Kmt2d C T 15: 98,741,020 (GRCm39) G4638R unknown Het
Lilrb4b T A 10: 51,357,829 (GRCm39) N174K possibly damaging Het
Ltbp2 G A 12: 84,837,864 (GRCm39) P1192L probably benign Het
Ltf T A 9: 110,868,003 (GRCm39) V615E probably damaging Het
Map7d1 G T 4: 126,130,478 (GRCm39) Q443K possibly damaging Het
Mapk9 A G 11: 49,745,095 (GRCm39) D3G probably benign Het
Nktr T G 9: 121,582,154 (GRCm39) S1424A unknown Het
Npas1 A G 7: 16,195,333 (GRCm39) S332P possibly damaging Het
Or13a25 T C 7: 140,247,547 (GRCm39) S109P possibly damaging Het
Or52n2c T C 7: 104,574,086 (GRCm39) Y295C probably damaging Het
Or5ak4 A G 2: 85,161,348 (GRCm39) I298T probably benign Het
Or6d12 T C 6: 116,492,791 (GRCm39) F18L possibly damaging Het
Or8b12b C A 9: 37,684,800 (GRCm39) P282T probably damaging Het
Pcdh8 A G 14: 80,005,182 (GRCm39) W948R probably damaging Het
Pde3a A G 6: 141,195,614 (GRCm39) E100G probably benign Het
Phrf1 T A 7: 140,836,466 (GRCm39) V246D unknown Het
Pitpnb A T 5: 111,530,876 (GRCm39) N223I probably damaging Het
Pkd1l3 A T 8: 110,394,207 (GRCm39) R2065* probably null Het
Prepl T C 17: 85,383,379 (GRCm39) D355G possibly damaging Het
Runx2 A G 17: 45,046,508 (GRCm39) V5A probably benign Het
Sema4g T A 19: 44,986,846 (GRCm39) V433D possibly damaging Het
Senp6 A G 9: 79,994,732 (GRCm39) K24E probably benign Het
Slc22a8 T A 19: 8,583,427 (GRCm39) S211T probably damaging Het
Slc34a2 A G 5: 53,221,217 (GRCm39) D221G possibly damaging Het
Tmprss11g A T 5: 86,637,166 (GRCm39) L323Q probably damaging Het
Tpcn1 T C 5: 120,687,988 (GRCm39) probably benign Het
Trim65 G A 11: 116,018,050 (GRCm39) T311I probably benign Het
Tub T C 7: 108,625,962 (GRCm39) F284L possibly damaging Het
Ube2j1 G A 4: 33,036,711 (GRCm39) V12I probably benign Het
Vmn2r101 A T 17: 19,809,161 (GRCm39) N97Y probably benign Het
Vmn2r49 C A 7: 9,722,835 (GRCm39) W146C probably damaging Het
Zfp628 T C 7: 4,922,153 (GRCm39) L125P 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
R9140:Sema6a UTSW 18 47,415,009 (GRCm39) missense probably benign
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'- CCCATGTGGTGTAGCGTTAC -3'
(R):5'- AACCCAGCTGTGTATTGCTCC -3'

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