Incidental Mutation 'R6307:Sema6a'
ID 509510
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 044412-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6307 (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 A at 47382231 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 772 (R772L)
Ref Sequence ENSEMBL: ENSMUSP00000121442 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000135790] [ENSMUST00000156422]
AlphaFold O35464
Predicted Effect probably damaging
Transcript: ENSMUST00000019791
AA Change: R772L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: R772L

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: R717L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: R717L

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: R746L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: R746L

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 probably damaging
Transcript: ENSMUST00000135790
AA Change: R789L

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: R789L

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: R772L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: R772L

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: 99.3%
  • 20x: 97.6%
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 T C 10: 79,843,221 (GRCm39) L1232P probably damaging Het
Akap6 A T 12: 53,188,351 (GRCm39) I1922F possibly damaging Het
Ankdd1a C T 9: 65,415,343 (GRCm39) A227T possibly damaging Het
Arpc5 T C 1: 152,647,206 (GRCm39) V103A possibly damaging Het
Atp9a C A 2: 168,510,090 (GRCm39) V430F probably benign Het
Bod1 A G 11: 31,616,932 (GRCm39) S110P probably damaging Het
Cacna1c C A 6: 118,590,914 (GRCm39) V1453F probably damaging Het
Capn8 T A 1: 182,435,264 (GRCm39) M414K probably damaging Het
Cbl A T 9: 44,069,809 (GRCm39) probably null Het
Ccdc42 A T 11: 68,479,106 (GRCm39) Q98L probably damaging Het
Ccn3 T C 15: 54,611,421 (GRCm39) probably null Het
Cd200 C A 16: 45,217,545 (GRCm39) V49L probably benign Het
Celsr1 A G 15: 85,812,531 (GRCm39) S2060P probably benign Het
Ces1g A T 8: 94,057,820 (GRCm39) H160Q possibly damaging Het
Chrnb2 G T 3: 89,668,831 (GRCm39) H161Q probably damaging Het
Ctns G A 11: 73,082,559 (GRCm39) T57I probably benign Het
Cyp3a25 A T 5: 145,931,766 (GRCm39) M114K possibly damaging Het
D630003M21Rik A G 2: 158,057,871 (GRCm39) F536L probably benign Het
Dcc C T 18: 71,943,826 (GRCm39) R275Q probably benign Het
Dmxl2 A T 9: 54,289,990 (GRCm39) H2508Q possibly damaging Het
Elf5 C A 2: 103,269,757 (GRCm39) Q113K probably damaging Het
Fam83a T G 15: 57,849,507 (GRCm39) V17G possibly damaging Het
Farsa T C 8: 85,587,674 (GRCm39) probably null Het
Fat2 G C 11: 55,172,106 (GRCm39) T2869S possibly damaging Het
Fgg A T 3: 82,920,283 (GRCm39) Q354L probably damaging Het
Folh1 T C 7: 86,372,517 (GRCm39) D679G probably damaging Het
Gbp4 T A 5: 105,270,975 (GRCm39) R83* probably null Het
Gm17482 T A 6: 115,204,311 (GRCm39) probably benign Het
Hmgxb4 T A 8: 75,749,927 (GRCm39) V481D possibly damaging Het
Ifi207 A C 1: 173,552,619 (GRCm39) Y926D probably damaging Het
Ikzf5 T A 7: 130,993,377 (GRCm39) N264Y probably damaging Het
Kat6a T A 8: 23,430,384 (GRCm39) M1913K unknown Het
Krt33b A T 11: 99,915,694 (GRCm39) C351S probably benign Het
Lrp1 T C 10: 127,427,944 (GRCm39) D543G probably damaging Het
Lrrfip2 C T 9: 111,053,021 (GRCm39) R339W probably damaging Het
Mapk3 T G 7: 126,363,454 (GRCm39) M276R probably benign Het
Mgst1 T C 6: 138,127,827 (GRCm39) V137A probably benign Het
Muc16 T C 9: 18,558,884 (GRCm39) T2470A unknown Het
Muc4 C T 16: 32,575,237 (GRCm39) S1274F possibly damaging Het
Myo5c A C 9: 75,180,198 (GRCm39) K713T possibly damaging Het
Myzap T C 9: 71,466,146 (GRCm39) D170G possibly damaging Het
Naa50 T C 16: 43,979,831 (GRCm39) V113A probably damaging Het
Neu3 T C 7: 99,462,929 (GRCm39) T265A probably benign Het
Nin T C 12: 70,061,631 (GRCm39) T2078A possibly damaging Het
Nomo1 G A 7: 45,683,260 (GRCm39) probably benign Het
Nprl3 A G 11: 32,189,828 (GRCm39) L273P probably damaging Het
Oaf T A 9: 43,136,216 (GRCm39) H120L possibly damaging Het
Or10s1 T C 9: 39,985,824 (GRCm39) S78P probably damaging Het
Or13p4 C T 4: 118,547,145 (GRCm39) R168H probably benign Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Or8k21 T C 2: 86,145,468 (GRCm39) H54R probably benign Het
Pcdhga3 T A 18: 37,809,674 (GRCm39) probably benign Het
Polq G A 16: 36,837,718 (GRCm39) probably null Het
Prdm8 C T 5: 98,333,162 (GRCm39) P243L possibly damaging Het
Prim2 T C 1: 33,701,373 (GRCm39) D138G probably benign Het
Prl2c5 A G 13: 13,365,175 (GRCm39) E107G probably benign Het
Prr14l T A 5: 32,984,869 (GRCm39) H1542L probably damaging Het
Rab26 T C 17: 24,749,072 (GRCm39) E203G probably damaging Het
Rtkn2 A T 10: 67,871,662 (GRCm39) H350L possibly damaging Het
Scara3 T C 14: 66,175,710 (GRCm39) D19G probably benign Het
Scn3a A G 2: 65,302,685 (GRCm39) S1254P probably damaging Het
Sdcbp A G 4: 6,385,059 (GRCm39) M93V probably benign Het
Slc5a7 T C 17: 54,584,006 (GRCm39) K428R probably benign Het
Sptbn2 G A 19: 4,774,674 (GRCm39) G109D probably damaging Het
Tmppe T C 9: 114,233,812 (GRCm39) L37P probably benign Het
Tuba1a T C 15: 98,849,410 (GRCm39) T56A probably benign Het
Tut4 T A 4: 108,412,817 (GRCm39) I1506N probably damaging Het
Vmn2r111 A G 17: 22,792,070 (GRCm39) I62T probably benign Het
Vmn2r73 A G 7: 85,506,828 (GRCm39) I828T probably damaging Het
Vmn2r79 T A 7: 86,686,976 (GRCm39) W786R probably damaging Het
Zp1 G A 19: 10,894,084 (GRCm39) T405M probably null 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
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'- CGCTCATTTTGGGCTGATCTAC -3'
(R):5'- CAAGCTCAGTGGCCTCTTTG -3'

Sequencing Primer
(F):5'- TGGGCTGATCTACGTACTCG -3'
(R):5'- AGTGGCCTCTTTGGGGACAC -3'
Posted On 2018-04-02