Incidental Mutation 'R6054:Sema6a'
ID 484340
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 044222-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6054 (G1)
Quality Score 225.009
Status Not validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 47416470 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Asparagine at position 386 (D386N)
Ref Sequence ENSEMBL: ENSMUSP00000111109 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect possibly damaging
Transcript: ENSMUST00000019791
AA Change: D386N

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: D386N

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 possibly damaging
Transcript: ENSMUST00000076043
AA Change: D386N

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: D386N

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 possibly damaging
Transcript: ENSMUST00000115449
AA Change: D386N

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: D386N

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 possibly damaging
Transcript: ENSMUST00000135790
AA Change: D386N

PolyPhen 2 Score 0.899 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: D386N

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 noncoding transcript
Transcript: ENSMUST00000141224
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151382
Predicted Effect possibly damaging
Transcript: ENSMUST00000156422
AA Change: D386N

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: D386N

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: 99.9%
  • 3x: 99.7%
  • 10x: 98.2%
  • 20x: 94.8%
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930562C15Rik T C 16: 4,653,729 (GRCm39) S93P unknown Het
Adam28 T A 14: 68,879,601 (GRCm39) N149I probably benign Het
Adam4 A C 12: 81,466,828 (GRCm39) F598V probably damaging Het
Adh5 A G 3: 138,151,136 (GRCm39) H33R possibly damaging Het
Apoh A G 11: 108,286,801 (GRCm39) N75S probably damaging Het
Arrdc5 T C 17: 56,601,420 (GRCm39) E235G possibly damaging Het
Atm T C 9: 53,371,173 (GRCm39) D2225G probably damaging Het
Atp6v0a1 C T 11: 100,930,715 (GRCm39) P514L possibly damaging Het
Brd9 T A 13: 74,088,860 (GRCm39) M195K probably damaging Het
Cacna1a T G 8: 85,283,414 (GRCm39) S755A probably damaging Het
Ccdc85c T A 12: 108,241,028 (GRCm39) H122L unknown Het
Ccs A T 19: 4,875,893 (GRCm39) D192E probably benign Het
Cd3e G A 9: 44,913,459 (GRCm39) T92M possibly damaging Het
Celsr2 A G 3: 108,314,279 (GRCm39) F1249L possibly damaging Het
Col16a1 G A 4: 129,955,515 (GRCm39) probably benign Het
Col17a1 A G 19: 47,668,859 (GRCm39) Y122H probably damaging Het
Col28a1 G A 6: 8,083,748 (GRCm39) P570S possibly damaging Het
Dchs2 A T 3: 83,253,543 (GRCm39) I2318L probably benign Het
Dhx35 T A 2: 158,660,219 (GRCm39) Y184N probably benign Het
Dmxl1 T G 18: 49,990,453 (GRCm39) N297K probably benign Het
Dsp G A 13: 38,351,585 (GRCm39) G135S probably benign Het
Efhb C T 17: 53,706,027 (GRCm39) V837I possibly damaging Het
Efs C T 14: 55,158,614 (GRCm39) D15N probably damaging Het
Fbxl19 C T 7: 127,351,681 (GRCm39) T314I probably damaging Het
Gm11595 A T 11: 99,663,474 (GRCm39) C69S unknown Het
Grxcr2 A G 18: 42,119,743 (GRCm39) V199A probably benign Het
Hadha T C 5: 30,328,682 (GRCm39) E468G probably benign Het
Hax1 GTCATCATCATCATCATC GTCATCATCATCATCATCATC 3: 89,905,247 (GRCm39) probably benign Het
Hps1 A T 19: 42,759,217 (GRCm39) V125E probably damaging Het
Hrg A T 16: 22,772,412 (GRCm39) T74S probably benign Het
Idh3a T C 9: 54,493,829 (GRCm39) probably null Het
Leng8 C A 7: 4,148,522 (GRCm39) probably null Het
Maml2 TCAGCAGCAGCAGCAGCAGC TCAGCAGCAGCAGCAGC 9: 13,532,695 (GRCm39) probably benign Het
Mctp2 T C 7: 71,908,851 (GRCm39) H154R probably benign Het
Megf6 A G 4: 154,347,636 (GRCm39) E777G probably benign Het
Miip A G 4: 147,950,135 (GRCm39) S154P probably benign Het
Mprip T C 11: 59,649,251 (GRCm39) V985A probably benign Het
Nmrk2 G A 10: 81,035,468 (GRCm39) R158W probably damaging Het
Nsd2 T C 5: 34,039,505 (GRCm39) S180P probably damaging Het
Oga A G 19: 45,764,571 (GRCm39) S190P probably damaging Het
Opa1 T G 16: 29,433,952 (GRCm39) S596A probably damaging Het
Or1ad1 G A 11: 50,875,631 (GRCm39) M34I probably benign Het
Or51b4 A G 7: 103,531,033 (GRCm39) V139A probably damaging Het
Pcdha2 A G 18: 37,073,857 (GRCm39) E496G probably damaging Het
Pcdhb5 T G 18: 37,454,133 (GRCm39) V171G probably damaging Het
Pramel6 A G 2: 87,339,003 (GRCm39) T68A probably benign Het
Ptprq T C 10: 107,418,219 (GRCm39) Y1719C probably damaging Het
Pzp T C 6: 128,490,727 (GRCm39) N412S probably benign Het
Rb1cc1 G T 1: 6,320,058 (GRCm39) R1159L probably benign Het
Rev3l T A 10: 39,700,146 (GRCm39) S1548T probably benign Het
Rora A G 9: 69,286,084 (GRCm39) I471M probably benign Het
Scube1 C A 15: 83,535,877 (GRCm39) V266L probably benign Het
Siglecf T A 7: 43,004,430 (GRCm39) L253Q probably damaging Het
Spata31d1b A G 13: 59,863,464 (GRCm39) H204R probably benign Het
Syt17 T C 7: 118,007,356 (GRCm39) T313A possibly damaging Het
Tbc1d32 T C 10: 56,038,304 (GRCm39) T578A possibly damaging Het
Trpm1 A G 7: 63,918,450 (GRCm39) S597G probably benign Het
Vmn2r9 T A 5: 108,996,126 (GRCm39) H174L probably damaging Het
Vrk2 A T 11: 26,436,975 (GRCm39) S281T probably benign Het
Wdr48 A G 9: 119,736,843 (GRCm39) D22G probably damaging Het
Zfp408 C A 2: 91,479,636 (GRCm39) V61L probably benign Het
Zfp652 G A 11: 95,640,689 (GRCm39) A205T 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
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'- ATGACAGGATCCGTGAACAC -3'
(R):5'- GGCAGTCCAGAGGAAATCTC -3'

Sequencing Primer
(F):5'- GATCCGTGAACACAAGATAAAGTC -3'
(R):5'- CCAGAGGAAATCTCAGCATGTTGTAC -3'
Posted On 2017-07-14