Incidental Mutation 'R9488:Sema6a'
ID 716781
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
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R9488 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 47437216 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 58 (I58N)
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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: I58N

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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: I58N

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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: I58N

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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000118655
Gene: ENSMUSG00000019647
AA Change: I58N

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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: I58N

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: I58N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: I58N

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: 99.6%
  • 20x: 98.9%
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930433I11Rik A T 7: 40,643,212 (GRCm39) I294L probably benign Het
Ankrd35 A T 3: 96,589,343 (GRCm39) K187N probably damaging Het
Arhgap40 C T 2: 158,391,571 (GRCm39) T631M possibly damaging Het
Arpin T C 7: 79,584,979 (GRCm39) Y5C probably damaging Het
B020011L13Rik A G 1: 117,728,724 (GRCm39) Y77C Het
Cdk17 A G 10: 93,044,066 (GRCm39) K2E probably damaging Het
Cdk18 A G 1: 132,049,260 (GRCm39) F86L probably benign Het
Cfap418 A G 4: 10,893,271 (GRCm39) D130G probably damaging Het
Clca4a T C 3: 144,659,532 (GRCm39) T775A probably damaging Het
Clvs2 T A 10: 33,389,301 (GRCm39) D313V possibly damaging Het
Col6a5 T C 9: 105,741,788 (GRCm39) Y2377C probably damaging Het
Drd2 T C 9: 49,311,094 (GRCm39) V115A probably damaging Het
Dsp A G 13: 38,377,218 (GRCm39) R1668G probably benign Het
Eif2d T A 1: 131,082,962 (GRCm39) V102E probably damaging Het
Fmo4 A G 1: 162,631,337 (GRCm39) V210A probably damaging Het
Galntl5 A G 5: 25,415,437 (GRCm39) R323G probably damaging Het
Git2 T C 5: 114,904,533 (GRCm39) T129A probably benign Het
Gm572 A G 4: 148,752,913 (GRCm39) H264R possibly damaging Het
Hnrnpll T C 17: 80,369,385 (GRCm39) T13A unknown Het
Ighv7-4 T C 12: 114,186,619 (GRCm39) Y51C probably damaging Het
Irag2 G A 6: 145,113,753 (GRCm39) R307Q probably damaging Het
Jam2 A G 16: 84,619,676 (GRCm39) D289G probably damaging Het
Krt27 A G 11: 99,239,535 (GRCm39) probably null Het
Lama5 T C 2: 179,823,234 (GRCm39) N2704S possibly damaging Het
Lhx8 A T 3: 154,033,764 (GRCm39) S70T possibly damaging Het
Lmo7 C A 14: 102,122,783 (GRCm39) T324N possibly damaging Het
Man2a1 A G 17: 65,040,734 (GRCm39) T907A possibly damaging Het
Map3k4 C T 17: 12,489,860 (GRCm39) A524T probably damaging Het
Mga C T 2: 119,795,304 (GRCm39) A2996V possibly damaging Het
Mybpc1 A T 10: 88,379,624 (GRCm39) M625K possibly damaging Het
Ncald T A 15: 37,372,369 (GRCm39) N159Y probably damaging Het
Nfasc T C 1: 132,527,866 (GRCm39) T832A possibly damaging Het
P2rx5 T A 11: 73,056,427 (GRCm39) I117N Het
Pcdhb3 C A 18: 37,435,416 (GRCm39) R461S possibly damaging Het
Polr1b T C 2: 128,967,417 (GRCm39) S937P probably damaging Het
Prep C A 10: 44,996,807 (GRCm39) Q362K Het
Prg4 T C 1: 150,327,024 (GRCm39) M342V probably benign Het
Prr14 A T 7: 127,073,687 (GRCm39) T184S possibly damaging Het
Prss58 A G 6: 40,874,382 (GRCm39) I98T probably benign Het
Pum3 T C 19: 27,394,188 (GRCm39) T361A probably damaging Het
Rsf1 GCGGCGGCG GCGGCGGCGTCGGCGGCG 7: 97,229,129 (GRCm39) probably benign Het
Sema4c A G 1: 36,591,067 (GRCm39) V424A probably benign Het
Slc13a3 T A 2: 165,250,851 (GRCm39) Y506F probably damaging Het
Slc15a2 A G 16: 36,579,651 (GRCm39) V365A probably benign Het
Slc39a5 G A 10: 128,233,628 (GRCm39) L290F probably damaging Het
Spata31f1a A G 4: 42,850,560 (GRCm39) V532A probably benign Het
Taf6l T C 19: 8,759,436 (GRCm39) T161A probably benign Het
Tbl2 T A 5: 135,187,471 (GRCm39) C243S probably benign Het
Tet2 A T 3: 133,193,103 (GRCm39) S444T probably benign Het
Thoc1 C T 18: 9,992,168 (GRCm39) L499F probably damaging Het
Tnc A G 4: 63,913,942 (GRCm39) V1290A probably damaging Het
Tnpo1 T C 13: 98,990,003 (GRCm39) D716G probably damaging Het
Tpp2 A T 1: 44,041,272 (GRCm39) K1236N probably benign Het
Tshr T C 12: 91,504,589 (GRCm39) V509A probably damaging Het
U2surp T C 9: 95,356,535 (GRCm39) T775A Het
Ubap2l T C 3: 89,928,656 (GRCm39) T486A probably benign Het
Usp28 C A 9: 48,935,288 (GRCm39) P457T probably damaging Het
Usp44 A G 10: 93,682,851 (GRCm39) I387V possibly damaging Het
Vmn1r225 A G 17: 20,722,793 (GRCm39) D78G probably damaging Het
Vps13b T C 15: 35,447,880 (GRCm39) M537T possibly damaging Het
Wdr6 G A 9: 108,453,182 (GRCm39) R234C probably damaging Het
Zfp1005 G A 2: 150,110,477 (GRCm39) G389D unknown Het
Zfp949 C A 9: 88,452,182 (GRCm39) T584N 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
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
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'- AGGATTGCTTGACAAACACAAGTAG -3'
(R):5'- ATGGTGGCATGGTCTGAATTAAAAC -3'

Sequencing Primer
(F):5'- GACAAACACAAGTAGGTTTTAGCTG -3'
(R):5'- TAAAACATGGTTTTGTTCTGTGGCCC -3'
Posted On 2022-07-18