Incidental Mutation 'R1593:Cntn6'
ID 175608
Institutional Source Beutler Lab
Gene Symbol Cntn6
Ensembl Gene ENSMUSG00000030092
Gene Name contactin 6
Synonyms NB-3
MMRRC Submission 039630-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.141) question?
Stock # R1593 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 104469751-104840367 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 104809541 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 525 (H525Q)
Ref Sequence ENSEMBL: ENSMUSP00000124025 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000089215] [ENSMUST00000161070] [ENSMUST00000162872]
AlphaFold Q9JMB8
Predicted Effect possibly damaging
Transcript: ENSMUST00000089215
AA Change: H525Q

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000086623
Gene: ENSMUSG00000030092
AA Change: H525Q

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: H453Q

PolyPhen 2 Score 0.343 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000124714
Gene: ENSMUSG00000030092
AA Change: H453Q

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 possibly damaging
Transcript: ENSMUST00000162872
AA Change: H525Q

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000124025
Gene: ENSMUSG00000030092
AA Change: H525Q

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
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.6%
  • 20x: 90.5%
Validation Efficiency
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acly A T 11: 100,372,581 (GRCm39) I902N possibly damaging Het
Acsl6 A G 11: 54,214,134 (GRCm39) D88G probably damaging Het
Adam1a A C 5: 121,657,706 (GRCm39) I529S probably benign Het
Ap3b1 T C 13: 94,638,435 (GRCm39) V838A unknown Het
Arrdc2 T C 8: 71,289,764 (GRCm39) Y280C probably damaging Het
Atg10 T C 13: 91,302,380 (GRCm39) T53A probably benign Het
Ccdc136 T C 6: 29,415,583 (GRCm39) S699P probably damaging Het
Cdc23 C A 18: 34,769,379 (GRCm39) V462L possibly damaging Het
Clcn6 C T 4: 148,099,051 (GRCm39) A431T probably benign Het
Ctr9 T C 7: 110,642,060 (GRCm39) F296S possibly damaging Het
Ctsq T A 13: 61,183,986 (GRCm39) probably null Het
Ehd1 A G 19: 6,348,330 (GRCm39) D436G Het
Epha6 A T 16: 60,245,267 (GRCm39) F311I probably damaging Het
Esrrg A T 1: 187,798,582 (GRCm39) T150S possibly damaging Het
Exoc2 C A 13: 31,040,744 (GRCm39) R758L possibly damaging Het
Exosc7 G C 9: 122,961,058 (GRCm39) V242L probably benign Het
Fcho2 T C 13: 98,921,315 (GRCm39) D190G possibly damaging Het
Fgd6 T C 10: 93,880,894 (GRCm39) S583P probably damaging Het
Frmd4a A G 2: 4,477,999 (GRCm39) Y60C probably damaging Het
Gldc A T 19: 30,091,150 (GRCm39) I815N probably damaging Het
Grm2 A T 9: 106,528,113 (GRCm39) L257Q probably damaging Het
Hectd3 C A 4: 116,854,217 (GRCm39) T289K possibly damaging Het
Itgb4 T C 11: 115,871,817 (GRCm39) V207A probably damaging Het
Lamb3 A G 1: 193,013,104 (GRCm39) E443G probably damaging Het
Meis2 T A 2: 115,830,745 (GRCm39) D256V probably damaging Het
Muc4 A G 16: 32,754,686 (GRCm38) N1520S probably benign Het
Nckap1l A G 15: 103,387,281 (GRCm39) R719G probably null Het
Or6c210 A T 10: 129,496,094 (GRCm39) R140* probably null Het
Pabpc6 A T 17: 9,886,742 (GRCm39) M603K probably damaging Het
Pcnx2 C A 8: 126,486,012 (GRCm39) R1862L probably benign Het
Pgap6 T A 17: 26,337,381 (GRCm39) I399N possibly damaging Het
Pon2 T C 6: 5,273,003 (GRCm39) D122G probably benign Het
Ppig T A 2: 69,579,425 (GRCm39) W378R unknown Het
Ralgapa1 T A 12: 55,817,488 (GRCm39) E389D probably damaging Het
Rapgef6 TG TGG 11: 54,437,223 (GRCm39) probably null Het
Rarg A G 15: 102,148,376 (GRCm39) F233L probably damaging Het
Rasgrp2 T C 19: 6,453,490 (GRCm39) F90L possibly damaging Het
Rrp12 T A 19: 41,851,680 (GRCm39) H1285L probably benign Het
Slc16a13 C A 11: 70,109,908 (GRCm39) A198S probably benign Het
Spag9 A G 11: 93,988,059 (GRCm39) D441G probably damaging Het
Stxbp5l A G 16: 36,936,414 (GRCm39) F1099S probably damaging Het
Tex19.1 T A 11: 121,038,079 (GRCm39) W146R probably damaging Het
Tmod3 T C 9: 75,418,445 (GRCm39) D197G probably benign Het
Tpp2 A G 1: 44,014,593 (GRCm39) H644R probably benign Het
Trpm2 A G 10: 77,778,910 (GRCm39) V352A possibly damaging Het
Tulp1 T C 17: 28,581,675 (GRCm39) K233E probably damaging Het
Vsir A G 10: 60,193,737 (GRCm39) T67A possibly damaging Het
Wdr49 T C 3: 75,304,248 (GRCm39) N487S probably benign Het
Zbtb20 A G 16: 43,429,786 (GRCm39) N99S probably damaging Het
Zfp583 C T 7: 6,320,008 (GRCm39) G335S probably benign Het
Zgrf1 T A 3: 127,354,675 (GRCm39) V98E possibly 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
R0960:Cntn6 UTSW 6 104,751,441 (GRCm39) missense probably benign 0.01
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
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'- ATTGGTGGTTCGCTCTGCCTTTAATAA -3'
(R):5'- GCTACAGCAGACAAGCGTTCTAGTGT -3'

Sequencing Primer
(F):5'- CGCTCTGCCTTTAATAATAGCATAC -3'
(R):5'- CCCAGATAGAGATTCTGCCTGTG -3'
Posted On 2014-04-24