Incidental Mutation 'R0960:Cntn6'
ID 81823
Institutional Source Beutler Lab
Gene Symbol Cntn6
Ensembl Gene ENSMUSG00000030092
Gene Name contactin 6
Synonyms NB-3
MMRRC Submission 039089-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.141) question?
Stock # R0960 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 104469751-104840367 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 104751441 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 294 (I294V)
Ref Sequence ENSEMBL: ENSMUSP00000124714 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000089215] [ENSMUST00000161070] [ENSMUST00000162872]
AlphaFold Q9JMB8
Predicted Effect probably benign
Transcript: ENSMUST00000089215
AA Change: I366V

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000086623
Gene: ENSMUSG00000030092
AA Change: I366V

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
IGc2 41 107 5.24e-7 SMART
IG 129 217 2.28e-7 SMART
IGc2 240 304 4e-12 SMART
IGc2 330 393 4.52e-11 SMART
IGc2 422 486 5.48e-10 SMART
IGc2 512 584 1.44e-4 SMART
FN3 598 684 2.17e-11 SMART
FN3 701 787 8.62e0 SMART
FN3 803 888 9.92e-6 SMART
FN3 903 983 8.17e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000161070
AA Change: I294V

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000124714
Gene: ENSMUSG00000030092
AA Change: I294V

DomainStartEndE-ValueType
SCOP:d1cs6a4 4 40 5e-4 SMART
IG 57 145 2.28e-7 SMART
IGc2 168 232 4e-12 SMART
IGc2 258 321 4.52e-11 SMART
IGc2 350 414 5.48e-10 SMART
IGc2 440 512 1.44e-4 SMART
FN3 526 612 2.17e-11 SMART
FN3 629 715 8.62e0 SMART
FN3 731 816 9.92e-6 SMART
FN3 831 911 8.17e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000162872
AA Change: I366V

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000124025
Gene: ENSMUSG00000030092
AA Change: I366V

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
IGc2 41 107 5.24e-7 SMART
IG 129 217 2.28e-7 SMART
IGc2 240 304 4e-12 SMART
IGc2 330 393 4.52e-11 SMART
IGc2 422 486 5.48e-10 SMART
IGc2 512 584 1.44e-4 SMART
FN3 598 684 2.17e-11 SMART
FN3 701 787 8.62e0 SMART
FN3 803 888 9.92e-6 SMART
FN3 903 983 8.17e0 SMART
Meta Mutation Damage Score 0.0597 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 99.0%
  • 10x: 97.8%
  • 20x: 96.0%
Validation Efficiency 98% (49/50)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for disruption of this gene display impaired coordination without any obvious morphological of physiological abnormalities in the brain. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810009A15Rik T C 19: 8,867,792 (GRCm39) V256A probably benign Het
4930433I11Rik A T 7: 40,642,480 (GRCm39) T141S probably benign Het
4930474N05Rik C A 14: 35,818,367 (GRCm39) H122N probably benign Het
Aamp T C 1: 74,320,304 (GRCm39) T341A possibly damaging Het
Adam26a A T 8: 44,021,800 (GRCm39) H563Q probably damaging Het
Ankrd13a G A 5: 114,924,868 (GRCm39) E118K probably benign Het
Asic5 A G 3: 81,913,847 (GRCm39) I174V probably benign Het
Atad2b G A 12: 5,056,593 (GRCm39) probably benign Het
Bub1b A G 2: 118,437,161 (GRCm39) I120V probably benign Het
Casp8 T C 1: 58,868,172 (GRCm39) probably null Het
Cdk5rap2 A G 4: 70,161,745 (GRCm39) Y254H probably benign Het
Clasp1 T C 1: 118,479,756 (GRCm39) I996T probably benign Het
Flnc A G 6: 29,441,511 (GRCm39) D431G probably damaging Het
Gm4884 T A 7: 40,692,232 (GRCm39) M67K possibly damaging Het
Hmx3 T C 7: 131,145,043 (GRCm39) Y118H probably benign Het
Hsf2bp C T 17: 32,226,743 (GRCm39) R204H probably damaging Het
Il12b G T 11: 44,299,315 (GRCm39) C128F probably damaging Het
Ints6 T C 14: 62,947,015 (GRCm39) M317V probably benign Het
Iqca1 C A 1: 90,070,453 (GRCm39) G133V probably null Het
Kcnh2 C T 5: 24,527,670 (GRCm39) R894H probably damaging Het
Kif27 T C 13: 58,471,781 (GRCm39) E769G probably damaging Het
Kif28 G A 1: 179,523,370 (GRCm39) Q987* probably null Het
Klhdc3 T C 17: 46,987,444 (GRCm39) H330R possibly damaging Het
Leo1 G A 9: 75,352,522 (GRCm39) E22K probably benign Het
Lpcat2 C T 8: 93,596,338 (GRCm39) T125M probably benign Het
Map1a A G 2: 121,132,124 (GRCm39) Y742C probably benign Het
Mllt6 C T 11: 97,555,772 (GRCm39) probably benign Het
Mpp2 A G 11: 101,952,411 (GRCm39) V354A possibly damaging Het
Mroh2a C A 1: 88,170,142 (GRCm39) A685D possibly damaging Het
Myo10 A G 15: 25,801,275 (GRCm39) E1488G probably damaging Het
Neb A G 2: 52,102,995 (GRCm39) V4461A probably benign Het
Nudcd1 G T 15: 44,291,047 (GRCm39) probably benign Het
Or10ag59 T C 2: 87,406,279 (GRCm39) Y284H probably benign Het
Or2w1b A C 13: 21,300,435 (GRCm39) D191A possibly damaging Het
Pde1a G A 2: 79,695,378 (GRCm39) probably benign Het
Sdha A T 13: 74,471,303 (GRCm39) probably benign Het
Selenoo T G 15: 88,980,957 (GRCm39) I432S probably benign Het
Sh3gl2 A T 4: 85,295,717 (GRCm39) I140F probably damaging Het
Svopl G T 6: 37,993,992 (GRCm39) Y346* probably null Het
Tbc1d17 C T 7: 44,497,852 (GRCm39) probably benign Het
Tlr3 A C 8: 45,850,452 (GRCm39) I815S probably damaging Het
Tmem25 T A 9: 44,706,809 (GRCm39) probably null Het
Tpd52 A T 3: 9,008,650 (GRCm39) probably null Het
Tspoap1 A T 11: 87,661,421 (GRCm39) probably benign Het
Txndc11 A T 16: 10,909,453 (GRCm39) D364E probably benign Het
Unc5cl G T 17: 48,766,624 (GRCm39) probably benign Het
Vmn1r13 A G 6: 57,186,996 (GRCm39) M52V probably benign Het
Zap70 T C 1: 36,818,254 (GRCm39) Y314H probably damaging Het
Other mutations in Cntn6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00547:Cntn6 APN 6 104,627,361 (GRCm39) missense probably damaging 0.99
IGL01331:Cntn6 APN 6 104,751,484 (GRCm39) missense probably damaging 1.00
IGL01619:Cntn6 APN 6 104,705,335 (GRCm39) splice site probably benign
IGL02028:Cntn6 APN 6 104,836,387 (GRCm39) missense probably damaging 0.99
IGL02420:Cntn6 APN 6 104,823,103 (GRCm39) critical splice donor site probably null
IGL02557:Cntn6 APN 6 104,751,496 (GRCm39) missense probably damaging 1.00
IGL03000:Cntn6 APN 6 104,781,347 (GRCm39) missense probably damaging 1.00
IGL03367:Cntn6 APN 6 104,781,299 (GRCm39) missense probably damaging 1.00
IGL03383:Cntn6 APN 6 104,753,418 (GRCm39) splice site probably benign
PIT4366001:Cntn6 UTSW 6 104,809,498 (GRCm39) missense probably benign 0.05
R0490:Cntn6 UTSW 6 104,810,879 (GRCm39) missense possibly damaging 0.91
R0583:Cntn6 UTSW 6 104,753,275 (GRCm39) missense possibly damaging 0.79
R0636:Cntn6 UTSW 6 104,840,109 (GRCm39) missense probably benign 0.00
R0654:Cntn6 UTSW 6 104,753,389 (GRCm39) missense probably benign 0.00
R1241:Cntn6 UTSW 6 104,809,470 (GRCm39) missense probably damaging 1.00
R1385:Cntn6 UTSW 6 104,838,861 (GRCm39) missense probably benign 0.07
R1401:Cntn6 UTSW 6 104,781,359 (GRCm39) missense possibly damaging 0.65
R1478:Cntn6 UTSW 6 104,753,389 (GRCm39) missense probably benign 0.00
R1542:Cntn6 UTSW 6 104,825,061 (GRCm39) missense probably damaging 1.00
R1593:Cntn6 UTSW 6 104,809,541 (GRCm39) missense possibly damaging 0.58
R1840:Cntn6 UTSW 6 104,751,441 (GRCm39) missense probably damaging 1.00
R2066:Cntn6 UTSW 6 104,838,783 (GRCm39) nonsense probably null
R2097:Cntn6 UTSW 6 104,838,910 (GRCm39) missense probably damaging 0.99
R2289:Cntn6 UTSW 6 104,545,989 (GRCm39) start gained probably benign
R2429:Cntn6 UTSW 6 104,627,526 (GRCm39) missense possibly damaging 0.96
R2967:Cntn6 UTSW 6 104,703,198 (GRCm39) missense probably benign 0.04
R4009:Cntn6 UTSW 6 104,810,783 (GRCm39) missense probably damaging 0.98
R4476:Cntn6 UTSW 6 104,749,522 (GRCm39) missense probably damaging 1.00
R4664:Cntn6 UTSW 6 104,705,245 (GRCm39) missense probably benign 0.20
R4666:Cntn6 UTSW 6 104,705,245 (GRCm39) missense probably benign 0.20
R4701:Cntn6 UTSW 6 104,781,321 (GRCm39) missense probably benign 0.01
R4780:Cntn6 UTSW 6 104,822,745 (GRCm39) missense probably damaging 1.00
R4854:Cntn6 UTSW 6 104,836,436 (GRCm39) missense possibly damaging 0.95
R4965:Cntn6 UTSW 6 104,751,435 (GRCm39) missense probably damaging 0.99
R5051:Cntn6 UTSW 6 104,749,558 (GRCm39) missense probably damaging 1.00
R5075:Cntn6 UTSW 6 104,809,991 (GRCm39) missense probably damaging 1.00
R5152:Cntn6 UTSW 6 104,546,074 (GRCm39) intron probably benign
R5291:Cntn6 UTSW 6 104,703,096 (GRCm39) missense probably damaging 1.00
R5388:Cntn6 UTSW 6 104,809,523 (GRCm39) missense probably damaging 1.00
R5852:Cntn6 UTSW 6 104,812,706 (GRCm39) missense probably damaging 0.97
R5937:Cntn6 UTSW 6 104,810,064 (GRCm39) missense possibly damaging 0.68
R5980:Cntn6 UTSW 6 104,825,093 (GRCm39) missense probably damaging 0.98
R6290:Cntn6 UTSW 6 104,744,851 (GRCm39) missense probably damaging 1.00
R6338:Cntn6 UTSW 6 104,703,100 (GRCm39) missense probably damaging 1.00
R6396:Cntn6 UTSW 6 104,627,461 (GRCm39) missense probably damaging 1.00
R6447:Cntn6 UTSW 6 104,836,409 (GRCm39) missense probably damaging 1.00
R6860:Cntn6 UTSW 6 104,838,907 (GRCm39) missense possibly damaging 0.95
R6871:Cntn6 UTSW 6 104,822,719 (GRCm39) frame shift probably null
R7012:Cntn6 UTSW 6 104,751,441 (GRCm39) missense probably benign 0.01
R7012:Cntn6 UTSW 6 104,703,223 (GRCm39) missense probably damaging 0.98
R7337:Cntn6 UTSW 6 104,627,491 (GRCm39) missense probably damaging 0.99
R7658:Cntn6 UTSW 6 104,627,444 (GRCm39) missense probably benign 0.29
R8133:Cntn6 UTSW 6 104,705,298 (GRCm39) missense probably benign 0.19
R8463:Cntn6 UTSW 6 104,749,580 (GRCm39) missense possibly damaging 0.64
R8909:Cntn6 UTSW 6 104,825,093 (GRCm39) missense probably benign 0.05
R9232:Cntn6 UTSW 6 104,815,781 (GRCm39) missense probably damaging 1.00
R9287:Cntn6 UTSW 6 104,809,471 (GRCm39) missense possibly damaging 0.89
R9454:Cntn6 UTSW 6 104,781,308 (GRCm39) missense possibly damaging 0.82
R9698:Cntn6 UTSW 6 104,810,044 (GRCm39) nonsense probably null
X0020:Cntn6 UTSW 6 104,744,845 (GRCm39) missense probably benign 0.00
Z1177:Cntn6 UTSW 6 104,809,545 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AACTGAAGGCTGCTGCTTCTCTAAC -3'
(R):5'- GGTTTGTACTCCAAGACCACCCAC -3'

Sequencing Primer
(F):5'- CAAGCAACACATTGTGAATTGGTC -3'
(R):5'- GTTCACAGGAAAATATCAGGTTCAG -3'
Posted On 2013-11-08