Incidental Mutation 'R1807:Sema6a'
ID 203573
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 039836-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1807 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 47378321-47504267 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 47409491 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 592 (V592A)
Ref Sequence ENSEMBL: ENSMUSP00000120011 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect probably benign
Transcript: ENSMUST00000019791
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647

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
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647

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
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647

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: V592A

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: V592A

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 probably benign
Transcript: ENSMUST00000156422
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647

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 0.0967 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.7%
  • 10x: 94.7%
  • 20x: 90.7%
Validation Efficiency 97% (77/79)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310061I04Rik C T 17: 36,205,961 (GRCm39) W27* probably null Het
4933430I17Rik T A 4: 62,460,993 (GRCm39) Y289* probably null Het
A3galt2 A G 4: 128,661,394 (GRCm39) I348V probably benign Het
Abca13 A G 11: 9,241,755 (GRCm39) Y1206C probably damaging Het
Adar T C 3: 89,642,172 (GRCm39) S18P probably benign Het
Akr1cl T C 1: 65,061,106 (GRCm39) D139G possibly damaging Het
Aldh1b1 A G 4: 45,802,873 (GRCm39) Y137C possibly damaging Het
Arsa T C 15: 89,359,525 (GRCm39) M86V possibly damaging Het
Atg9b C A 5: 24,592,055 (GRCm39) R648L probably damaging Het
Atrn A G 2: 130,824,692 (GRCm39) N1042S possibly damaging Het
Ccdc6 T A 10: 70,010,989 (GRCm39) D325E possibly damaging Het
Cdk12 T C 11: 98,101,203 (GRCm39) S354P unknown Het
Chst3 T A 10: 60,022,130 (GRCm39) Y239F probably benign Het
Cilp2 C A 8: 70,334,844 (GRCm39) R718L probably damaging Het
Col27a1 A G 4: 63,249,586 (GRCm39) probably benign Het
Ctbp2 T C 7: 132,616,137 (GRCm39) N266S probably benign Het
Ctnnd2 T C 15: 30,620,017 (GRCm39) V123A probably damaging Het
Cyria G A 12: 12,411,505 (GRCm39) R123Q probably benign Het
D7Ertd443e T A 7: 133,895,034 (GRCm39) E552V probably null Het
Dcst1 T A 3: 89,260,848 (GRCm39) H516L probably damaging Het
Depp1 G A 6: 116,628,683 (GRCm39) V9M possibly damaging Het
Drd2 C T 9: 49,316,367 (GRCm39) L376F probably damaging Het
Edn1 A G 13: 42,460,270 (GRCm39) N175S probably damaging Het
Eipr1 G T 12: 28,816,838 (GRCm39) G65V probably damaging Het
Epha4 G A 1: 77,351,541 (GRCm39) P905S probably benign Het
Erbb2 T C 11: 98,319,680 (GRCm39) Y591H probably damaging Het
Fam135b G A 15: 71,335,761 (GRCm39) R478C probably benign Het
Fat2 T C 11: 55,180,085 (GRCm39) T1419A probably damaging Het
Flnb C T 14: 7,934,645 (GRCm38) T2239I probably benign Het
Gm7713 T C 15: 59,866,320 (GRCm39) noncoding transcript Het
Hsf5 C T 11: 87,548,168 (GRCm39) P617L probably benign Het
Kcnk12 C A 17: 88,053,468 (GRCm39) R398L probably benign Het
Kif21b T A 1: 136,075,531 (GRCm39) N219K possibly damaging Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Klra5 A T 6: 129,876,383 (GRCm39) F141L probably benign Het
Lmtk3 C T 7: 45,442,702 (GRCm39) P462S probably benign Het
Mast2 A G 4: 116,167,938 (GRCm39) probably benign Het
Me1 T A 9: 86,532,932 (GRCm39) T197S probably damaging Het
Msr1 T A 8: 40,072,948 (GRCm39) Q267L probably benign Het
Nfic T C 10: 81,240,819 (GRCm39) T328A probably benign Het
Nphp3 G A 9: 103,897,940 (GRCm39) D390N probably benign Het
Nr2e1 T A 10: 42,458,905 (GRCm39) probably null Het
Nt5el A T 13: 105,218,744 (GRCm39) Q26L probably benign Het
Or52e19b T A 7: 103,032,790 (GRCm39) N140Y probably benign Het
Or5t9 T A 2: 86,659,445 (GRCm39) F116L probably benign Het
Pard6b T C 2: 167,929,332 (GRCm39) L46P probably damaging Het
Prkaa1 T A 15: 5,173,436 (GRCm39) L20Q probably damaging Het
Rapgefl1 T C 11: 98,736,815 (GRCm39) probably null Het
Recql5 T C 11: 115,785,941 (GRCm39) K611E possibly damaging Het
Rexo1 A T 10: 80,378,413 (GRCm39) I1180N possibly damaging Het
Rnf26rt A G 6: 76,474,397 (GRCm39) V73A probably benign Het
Rph3a T C 5: 121,083,456 (GRCm39) N605D probably damaging Het
Skint11 A T 4: 114,051,893 (GRCm39) R80S probably benign Het
Smpdl3a C A 10: 57,677,118 (GRCm39) P72H probably damaging Het
Sobp T G 10: 43,036,822 (GRCm39) M39L possibly damaging Het
Sparcl1 T A 5: 104,233,627 (GRCm39) Y574F probably damaging Het
Spns3 C T 11: 72,429,166 (GRCm39) W206* probably null Het
Srf A G 17: 46,864,685 (GRCm39) V190A possibly damaging Het
Stag1 T G 9: 100,790,719 (GRCm39) H742Q probably benign Het
Strn3 A T 12: 51,673,986 (GRCm39) S542T probably benign Het
Synpo2 T C 3: 122,873,906 (GRCm39) E1020G possibly damaging Het
Tcerg1l T A 7: 137,996,826 (GRCm39) H137L probably benign Het
Tlr12 A T 4: 128,511,229 (GRCm39) D340E probably benign Het
Tmem130 T A 5: 144,692,174 (GRCm39) T77S probably benign Het
Tmem143 C A 7: 45,547,037 (GRCm39) R68S probably damaging Het
Tnrc6a CTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT CTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT 7: 122,761,669 (GRCm39) probably benign Het
Trem1 G T 17: 48,548,663 (GRCm39) G67* probably null Het
Tsc1 A G 2: 28,576,125 (GRCm39) D978G probably benign Het
Txndc9 A T 1: 38,033,096 (GRCm39) H95Q probably damaging Het
Yju2b C T 8: 84,986,936 (GRCm39) R187Q probably damaging Het
Zfp35 T A 18: 24,136,986 (GRCm39) N443K 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
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
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'- CTCCTTAACTGTCTCATGTAAGCAG -3'
(R):5'- GAGTGTGCAGCCAAGTAACC -3'

Sequencing Primer
(F):5'- GGGCCCTGAAGTAACAAA -3'
(R):5'- CAGATTCCTTCGTGGCACTGAATG -3'
Posted On 2014-06-23