Incidental Mutation 'R1721:Sema6c'
ID 191443
Institutional Source Beutler Lab
Gene Symbol Sema6c
Ensembl Gene ENSMUSG00000038777
Gene Name sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C
Synonyms Sema Y, Semay
MMRRC Submission 039753-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.303) question?
Stock # R1721 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 95067768-95081335 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 95078099 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 492 (I492F)
Ref Sequence ENSEMBL: ENSMUSP00000144039 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000090821] [ENSMUST00000090823] [ENSMUST00000107217] [ENSMUST00000131620] [ENSMUST00000168321] [ENSMUST00000202315] [ENSMUST00000204709] [ENSMUST00000142449]
AlphaFold Q9WTM3
Predicted Effect probably damaging
Transcript: ENSMUST00000090821
AA Change: I492F

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: I492F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 488 2.55e-165 SMART
transmembrane domain 604 626 N/A INTRINSIC
low complexity region 627 638 N/A INTRINSIC
low complexity region 646 658 N/A INTRINSIC
low complexity region 660 669 N/A INTRINSIC
low complexity region 693 709 N/A INTRINSIC
low complexity region 744 761 N/A INTRINSIC
low complexity region 907 924 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000090823
AA Change: I492F

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: I492F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 488 2.55e-165 SMART
low complexity region 591 603 N/A INTRINSIC
transmembrane domain 636 658 N/A INTRINSIC
low complexity region 659 670 N/A INTRINSIC
low complexity region 678 690 N/A INTRINSIC
low complexity region 692 701 N/A INTRINSIC
low complexity region 725 741 N/A INTRINSIC
low complexity region 776 793 N/A INTRINSIC
low complexity region 939 956 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000107217
AA Change: I452F

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: I452F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 448 1.23e-126 SMART
low complexity region 551 563 N/A INTRINSIC
transmembrane domain 596 618 N/A INTRINSIC
low complexity region 619 630 N/A INTRINSIC
low complexity region 638 650 N/A INTRINSIC
low complexity region 652 661 N/A INTRINSIC
low complexity region 685 701 N/A INTRINSIC
low complexity region 736 753 N/A INTRINSIC
low complexity region 899 916 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126597
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130662
Predicted Effect probably benign
Transcript: ENSMUST00000131620
SMART Domains Protein: ENSMUSP00000138154
Gene: ENSMUSG00000038777

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000168321
AA Change: I492F

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: I492F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 488 2.55e-165 SMART
transmembrane domain 604 626 N/A INTRINSIC
low complexity region 627 638 N/A INTRINSIC
low complexity region 646 658 N/A INTRINSIC
low complexity region 660 669 N/A INTRINSIC
low complexity region 693 709 N/A INTRINSIC
low complexity region 744 761 N/A INTRINSIC
low complexity region 907 924 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000202315
AA Change: I492F

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: I492F

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 488 2.55e-165 SMART
transmembrane domain 604 626 N/A INTRINSIC
low complexity region 627 638 N/A INTRINSIC
low complexity region 646 658 N/A INTRINSIC
low complexity region 660 669 N/A INTRINSIC
low complexity region 693 709 N/A INTRINSIC
low complexity region 744 761 N/A INTRINSIC
low complexity region 907 924 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134125
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141607
Predicted Effect probably benign
Transcript: ENSMUST00000204709
SMART Domains Protein: ENSMUSP00000144702
Gene: ENSMUSG00000038777

DomainStartEndE-ValueType
low complexity region 10 20 N/A INTRINSIC
PDB:3OKY|B 25 117 8e-8 PDB
Blast:Sema 62 119 9e-34 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000142449
SMART Domains Protein: ENSMUSP00000123457
Gene: ENSMUSG00000038777

DomainStartEndE-ValueType
signal peptide 1 25 N/A INTRINSIC
Sema 62 488 2.55e-165 SMART
low complexity region 591 603 N/A INTRINSIC
transmembrane domain 636 658 N/A INTRINSIC
low complexity region 659 670 N/A INTRINSIC
low complexity region 678 690 N/A INTRINSIC
low complexity region 692 701 N/A INTRINSIC
low complexity region 725 741 N/A INTRINSIC
low complexity region 776 793 N/A INTRINSIC
low complexity region 939 956 N/A INTRINSIC
Meta Mutation Damage Score 0.0989 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.1%
Validation Efficiency 99% (87/88)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a targeted mutation display a decrease in pain threshold. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acin1 A T 14: 54,901,995 (GRCm39) V559E probably benign Het
Adamts20 A G 15: 94,236,340 (GRCm39) F844L probably benign Het
Adcy5 C A 16: 35,118,794 (GRCm39) D1048E probably damaging Het
Agrn A T 4: 156,259,630 (GRCm39) C768* probably null Het
Aldh18a1 G T 19: 40,553,282 (GRCm39) Q487K probably damaging Het
Aldh3b1 G A 19: 3,971,271 (GRCm39) probably benign Het
Asb18 T G 1: 89,896,302 (GRCm39) D246A probably benign Het
Atp2b1 T C 10: 98,832,750 (GRCm39) V417A probably damaging Het
Bcl2l15 A G 3: 103,745,914 (GRCm39) probably null Het
Brd10 A T 19: 29,720,998 (GRCm39) S743T probably damaging Het
Cage1 T A 13: 38,207,309 (GRCm39) K285* probably null Het
Ccn2 A C 10: 24,472,695 (GRCm39) T202P probably damaging Het
Cldn17 A G 16: 88,303,444 (GRCm39) L95P probably damaging Het
Cldn20 A T 17: 3,583,157 (GRCm39) D110V probably damaging Het
Cnot10 T C 9: 114,444,067 (GRCm39) T443A probably benign Het
Col14a1 T A 15: 55,310,858 (GRCm39) probably benign Het
Col23a1 T C 11: 51,418,716 (GRCm39) Y135H unknown Het
Cse1l T C 2: 166,768,331 (GRCm39) S210P probably damaging Het
Cspg4 T G 9: 56,796,027 (GRCm39) V1254G probably damaging Het
Dip2c A G 13: 9,709,404 (GRCm39) T1415A probably damaging Het
Epc2 A G 2: 49,422,117 (GRCm39) Y337C probably damaging Het
Epha2 A G 4: 141,049,963 (GRCm39) S799G probably damaging Het
Fndc10 A G 4: 155,779,355 (GRCm39) Y133C probably damaging Het
Gli3 G T 13: 15,900,882 (GRCm39) S1423I probably benign Het
Gm6034 A T 17: 36,354,045 (GRCm39) probably benign Het
Gmip A G 8: 70,263,882 (GRCm39) S109G probably damaging Het
Grik2 C A 10: 49,399,842 (GRCm39) W296L possibly damaging Het
Gucy2d T A 7: 98,103,268 (GRCm39) L504H probably damaging Het
Il6 T A 5: 30,218,490 (GRCm39) Y46N possibly damaging Het
Ints8 C A 4: 11,241,684 (GRCm39) C253F probably damaging Het
Itga9 A G 9: 118,527,374 (GRCm39) probably benign Het
Kcna7 T C 7: 45,056,345 (GRCm39) V187A possibly damaging Het
Kdm5b G T 1: 134,540,919 (GRCm39) probably benign Het
Knl1 T G 2: 118,906,815 (GRCm39) S1635A probably damaging Het
Lce1b A G 3: 92,563,318 (GRCm39) S72P unknown Het
Lox T G 18: 52,653,983 (GRCm39) probably null Het
Mdc1 A G 17: 36,158,718 (GRCm39) D366G possibly damaging Het
Meiob T C 17: 25,053,021 (GRCm39) C344R probably damaging Het
Mier2 A G 10: 79,384,664 (GRCm39) V150A probably damaging Het
Mon2 A T 10: 122,867,002 (GRCm39) M551K probably damaging Het
Mrps15 A G 4: 125,945,187 (GRCm39) T125A probably benign Het
Mtmr14 A G 6: 113,230,693 (GRCm39) H99R probably damaging Het
Mup4 A G 4: 59,960,598 (GRCm39) M1T probably null Het
Mup5 G A 4: 61,750,607 (GRCm39) R179* probably null Het
Ncoa3 T G 2: 165,911,221 (GRCm39) V1326G possibly damaging Het
Noa1 A T 5: 77,455,428 (GRCm39) N429K probably benign Het
Nrxn1 C T 17: 90,469,832 (GRCm39) A241T probably damaging Het
Or1p1 A T 11: 74,180,126 (GRCm39) Y218F probably damaging Het
Or2t49 C T 11: 58,392,765 (GRCm39) V206M probably damaging Het
Pcdh9 G A 14: 94,125,471 (GRCm39) S233L probably damaging Het
Peg3 C A 7: 6,712,900 (GRCm39) S774I possibly damaging Het
Phyh A G 2: 4,942,620 (GRCm39) K321R probably null Het
Plcg1 T A 2: 160,573,840 (GRCm39) M35K probably damaging Het
Pnisr C T 4: 21,874,086 (GRCm39) probably benign Het
Ppargc1b T A 18: 61,440,275 (GRCm39) probably null Het
Prcd A C 11: 116,548,371 (GRCm39) S27R probably benign Het
Prx T A 7: 27,216,948 (GRCm39) M622K probably benign Het
Psmd1 T A 1: 85,999,567 (GRCm39) D51E probably damaging Het
Psmd13 C T 7: 140,463,430 (GRCm39) T38I probably damaging Het
Ptprf A C 4: 118,082,096 (GRCm39) D1047E possibly damaging Het
Rai14 C A 15: 10,633,314 (GRCm39) Q25H probably damaging Het
Riiad1 G A 3: 94,380,176 (GRCm39) P40S possibly damaging Het
Rnft1 T A 11: 86,377,096 (GRCm39) N53K probably benign Het
Scn4a C T 11: 106,211,646 (GRCm39) R1457H probably benign Het
Shbg T C 11: 69,505,798 (GRCm39) H403R probably damaging Het
Slc15a5 A T 6: 138,049,845 (GRCm39) probably benign Het
Slc38a1 G A 15: 96,485,016 (GRCm39) T221M probably damaging Het
Slc6a16 T A 7: 44,910,600 (GRCm39) V375E possibly damaging Het
Slc6a17 T A 3: 107,379,492 (GRCm39) M559L probably damaging Het
Slmap A G 14: 26,181,373 (GRCm39) probably benign Het
Sorcs2 G A 5: 36,184,092 (GRCm39) R965W probably damaging Het
St8sia4 C A 1: 95,581,394 (GRCm39) R116L probably damaging Het
Tcaf1 A C 6: 42,652,272 (GRCm39) S737A possibly damaging Het
Thbs2 T A 17: 14,899,072 (GRCm39) Y676F probably benign Het
Tmod2 A G 9: 75,493,324 (GRCm39) probably benign Het
Trim75 T C 8: 65,435,391 (GRCm39) probably null Het
Ubr5 A T 15: 38,042,090 (GRCm39) S169T probably benign Het
Usp54 A T 14: 20,633,508 (GRCm39) Y37* probably null Het
Vill T C 9: 118,895,082 (GRCm39) F100S probably damaging Het
Vstm5 A G 9: 15,168,663 (GRCm39) R76G probably benign Het
Zfp608 T C 18: 55,032,321 (GRCm39) T540A probably benign Het
Zfp947 A C 17: 22,365,184 (GRCm39) N163K probably benign Het
Zfyve26 T C 12: 79,308,573 (GRCm39) H228R possibly damaging Het
Other mutations in Sema6c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01547:Sema6c APN 3 95,079,709 (GRCm39) missense probably damaging 1.00
IGL01631:Sema6c APN 3 95,077,714 (GRCm39) missense probably benign 0.10
IGL01799:Sema6c APN 3 95,078,142 (GRCm39) missense probably damaging 1.00
IGL02237:Sema6c APN 3 95,077,430 (GRCm39) missense probably damaging 1.00
IGL02852:Sema6c APN 3 95,077,295 (GRCm39) splice site probably benign
IGL02874:Sema6c APN 3 95,077,688 (GRCm39) missense probably damaging 1.00
IGL03003:Sema6c APN 3 95,076,925 (GRCm39) missense probably damaging 1.00
BB005:Sema6c UTSW 3 95,079,620 (GRCm39) missense probably damaging 1.00
BB015:Sema6c UTSW 3 95,079,620 (GRCm39) missense probably damaging 1.00
PIT4418001:Sema6c UTSW 3 95,077,401 (GRCm39) missense possibly damaging 0.57
R0558:Sema6c UTSW 3 95,076,002 (GRCm39) missense probably damaging 1.00
R0582:Sema6c UTSW 3 95,076,508 (GRCm39) missense probably damaging 1.00
R0590:Sema6c UTSW 3 95,079,934 (GRCm39) missense probably damaging 1.00
R0685:Sema6c UTSW 3 95,080,021 (GRCm39) missense possibly damaging 0.46
R1056:Sema6c UTSW 3 95,078,527 (GRCm39) missense probably benign 0.15
R1867:Sema6c UTSW 3 95,078,099 (GRCm39) missense probably damaging 0.98
R1868:Sema6c UTSW 3 95,078,124 (GRCm39) missense probably damaging 0.99
R2016:Sema6c UTSW 3 95,078,545 (GRCm39) missense probably benign 0.00
R2343:Sema6c UTSW 3 95,074,394 (GRCm39) missense probably damaging 1.00
R2898:Sema6c UTSW 3 95,080,129 (GRCm39) missense probably damaging 1.00
R4095:Sema6c UTSW 3 95,080,505 (GRCm39) missense probably benign 0.03
R4999:Sema6c UTSW 3 95,075,674 (GRCm39) missense probably damaging 1.00
R5263:Sema6c UTSW 3 95,080,463 (GRCm39) missense probably benign 0.02
R6914:Sema6c UTSW 3 95,080,519 (GRCm39) missense probably benign 0.00
R6942:Sema6c UTSW 3 95,080,519 (GRCm39) missense probably benign 0.00
R7104:Sema6c UTSW 3 95,076,156 (GRCm39) missense possibly damaging 0.95
R7524:Sema6c UTSW 3 95,074,371 (GRCm39) missense probably benign 0.20
R7724:Sema6c UTSW 3 95,080,510 (GRCm39) missense probably damaging 1.00
R7928:Sema6c UTSW 3 95,079,620 (GRCm39) missense probably damaging 1.00
R8045:Sema6c UTSW 3 95,080,535 (GRCm39) missense probably benign 0.27
R8243:Sema6c UTSW 3 95,079,916 (GRCm39) missense probably damaging 1.00
R8790:Sema6c UTSW 3 95,075,341 (GRCm39) missense probably benign 0.34
R9607:Sema6c UTSW 3 95,076,545 (GRCm39) missense probably benign 0.03
R9653:Sema6c UTSW 3 95,080,525 (GRCm39) missense probably benign 0.40
Z1177:Sema6c UTSW 3 95,075,639 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGATTGATGCCTACAGCCATGCC -3'
(R):5'- TCCTACTAACCCCGAAAGTGTAGCC -3'

Sequencing Primer
(F):5'- ACTTGGTGAGAAGCTCCAC -3'
(R):5'- CCAGGCAGCATGGAACTTAG -3'
Posted On 2014-05-14