Incidental Mutation 'R6885:Cntn1'
ID 536811
Institutional Source Beutler Lab
Gene Symbol Cntn1
Ensembl Gene ENSMUSG00000055022
Gene Name contactin 1
Synonyms F3cam, usl, CNTN
MMRRC Submission 045031-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6885 (G1)
Quality Score 225.009
Status Validated
Chromosome 15
Chromosomal Location 91949034-92239834 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 92140980 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000133063 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000109] [ENSMUST00000068378] [ENSMUST00000169825]
AlphaFold P12960
Predicted Effect probably null
Transcript: ENSMUST00000000109
SMART Domains Protein: ENSMUSP00000000109
Gene: ENSMUSG00000055022

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
IGc2 56 121 4.07e-4 SMART
IG 143 232 1.25e-4 SMART
IGc2 254 317 1.24e-17 SMART
IGc2 343 398 4.22e-11 SMART
IGc2 427 491 2.52e-9 SMART
IG 511 603 3.51e-8 SMART
FN3 606 692 6.69e-12 SMART
FN3 709 795 1.17e-2 SMART
FN3 811 892 1.16e-6 SMART
FN3 907 987 2.46e-1 SMART
low complexity region 995 1018 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000068378
SMART Domains Protein: ENSMUSP00000067842
Gene: ENSMUSG00000055022

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
IGc2 56 121 4.07e-4 SMART
IG 143 232 1.25e-4 SMART
IGc2 254 317 1.24e-17 SMART
IGc2 343 398 4.22e-11 SMART
IGc2 427 491 2.52e-9 SMART
IG 511 603 3.51e-8 SMART
FN3 606 692 6.69e-12 SMART
FN3 709 795 1.17e-2 SMART
FN3 811 892 1.16e-6 SMART
FN3 907 987 2.46e-1 SMART
low complexity region 995 1018 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000169825
SMART Domains Protein: ENSMUSP00000133063
Gene: ENSMUSG00000055022

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
IGc2 56 121 4.07e-4 SMART
IG 143 232 1.25e-4 SMART
IGc2 254 317 1.24e-17 SMART
IGc2 343 398 4.22e-11 SMART
IGc2 427 491 2.52e-9 SMART
IG 511 603 3.51e-8 SMART
FN3 606 692 6.69e-12 SMART
FN3 709 795 1.17e-2 SMART
FN3 811 892 1.16e-6 SMART
FN3 907 987 2.46e-1 SMART
low complexity region 995 1018 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.3%
Validation Efficiency 98% (58/59)
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. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Mutations of this gene result in growth retardation, progressive ataxia and death prior to weaning. A targeted null mutation, but not a spontaneous mutation, causes a small cerebellum with abnormalities of the molecular layer and abnormal Purkinje cellaxon morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A G 7: 120,119,332 (GRCm39) I1025M probably benign Het
Adamtsl5 T A 10: 80,179,465 (GRCm39) T164S probably benign Het
Ankar C T 1: 72,682,195 (GRCm39) A1239T unknown Het
Aox4 A T 1: 58,303,537 (GRCm39) S1192C probably damaging Het
Atl2 T C 17: 80,159,982 (GRCm39) D68G probably damaging Het
Btnl4 T C 17: 34,691,919 (GRCm39) I228V probably benign Het
Catsper4 T C 4: 133,942,460 (GRCm39) T231A probably benign Het
Ccl12 A T 11: 81,993,523 (GRCm39) T54S probably damaging Het
Cog5 T A 12: 31,944,198 (GRCm39) D694E probably damaging Het
Crat T A 2: 30,305,208 (GRCm39) probably benign Het
Crot T C 5: 9,023,635 (GRCm39) T418A probably benign Het
Cubn G A 2: 13,323,089 (GRCm39) P2826L probably damaging Het
Dnah17 A G 11: 117,981,598 (GRCm39) F1698L possibly damaging Het
Dock8 T A 19: 25,124,742 (GRCm39) D1019E possibly damaging Het
Eps15 A G 4: 109,166,361 (GRCm39) N85D probably damaging Het
Exoc1 T C 5: 76,706,889 (GRCm39) S457P probably damaging Het
Ext1 G A 15: 52,965,088 (GRCm39) T426I probably damaging Het
Fat1 T C 8: 45,405,489 (GRCm39) S747P possibly damaging Het
Gas7 A G 11: 67,574,213 (GRCm39) D396G probably damaging Het
Gm5114 G T 7: 39,057,580 (GRCm39) R680S probably benign Het
Gpcpd1 A T 2: 132,395,994 (GRCm39) L94M possibly damaging Het
Gse1 C A 8: 120,956,221 (GRCm39) probably benign Het
Hmgb1 T C 5: 148,987,471 (GRCm39) E26G probably benign Het
Incenp C T 19: 9,852,496 (GRCm39) R714Q unknown Het
Krt73 T C 15: 101,704,833 (GRCm39) E351G probably damaging Het
Ksr1 A G 11: 78,938,121 (GRCm39) probably null Het
Lpin2 T G 17: 71,522,145 (GRCm39) S60A probably damaging Het
Lrrc71 T C 3: 87,649,927 (GRCm39) probably null Het
Mafb A G 2: 160,207,939 (GRCm39) S220P possibly damaging Het
Maml3 TCTGCTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGCTGTTGCTGCTGCTGC TCTGCTGCTGCTGCTGCTGCTGTTGCTGCTGCTGCTGCTGTTGCTGCTGCTGC 3: 51,605,000 (GRCm39) Het
Mcmbp T C 7: 128,326,833 (GRCm39) probably null Het
Or1e30 A T 11: 73,677,926 (GRCm39) H54L possibly damaging Het
Or4s2 A G 2: 88,473,941 (GRCm39) T277A probably damaging Het
Paqr9 T C 9: 95,442,096 (GRCm39) S29P probably benign Het
Parm1 A G 5: 91,742,069 (GRCm39) T146A possibly damaging Het
Pgm2 T A 5: 64,261,221 (GRCm39) F238L probably benign Het
Pigv A T 4: 133,392,792 (GRCm39) F126Y probably damaging Het
Pitx2 T C 3: 129,012,257 (GRCm39) M222T probably damaging Het
Plekhg6 T C 6: 125,355,693 (GRCm39) N37S probably benign Het
Pramel25 T C 4: 143,520,103 (GRCm39) C116R probably damaging Het
Psme4 A T 11: 30,784,307 (GRCm39) K961* probably null Het
Rbpj T C 5: 53,810,493 (GRCm39) W392R probably damaging Het
Reg3a T A 6: 78,358,038 (GRCm39) probably null Het
Rfc3 C T 5: 151,571,749 (GRCm39) S85N probably benign Het
Rtn3 T C 19: 7,435,696 (GRCm39) T80A probably benign Het
Sash1 T C 10: 8,659,985 (GRCm39) T195A probably damaging Het
Ska1 A G 18: 74,339,910 (GRCm39) V12A probably benign Het
Slc25a1 A G 16: 17,745,294 (GRCm39) V80A probably benign Het
Slc26a5 A T 5: 22,039,342 (GRCm39) V217D probably damaging Het
Slc46a1 A G 11: 78,357,805 (GRCm39) D286G probably benign Het
Spata2l A T 8: 123,962,297 (GRCm39) L88Q probably damaging Het
Sptbn1 T G 11: 30,088,634 (GRCm39) Q876P probably benign Het
Tenm2 T A 11: 35,914,407 (GRCm39) I2377F possibly damaging Het
Thbs4 A T 13: 92,899,377 (GRCm39) D539E probably damaging Het
Tmem154 T A 3: 84,599,813 (GRCm39) C162S possibly damaging Het
Tpcn1 T C 5: 120,682,502 (GRCm39) E502G probably benign Het
Traf7 G A 17: 24,731,266 (GRCm39) R257C probably benign Het
Tsc22d2 T C 3: 58,323,629 (GRCm39) Y174H probably damaging Het
Usp8 A G 2: 126,594,230 (GRCm39) E802G probably damaging Het
Vmn1r5 T C 6: 56,963,042 (GRCm39) V239A possibly damaging Het
Vmn2r99 T A 17: 19,600,457 (GRCm39) S494T possibly damaging Het
Zbtb38 A G 9: 96,568,517 (GRCm39) F856L probably damaging Het
Other mutations in Cntn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00158:Cntn1 APN 15 92,148,758 (GRCm39) missense possibly damaging 0.92
IGL01109:Cntn1 APN 15 92,237,458 (GRCm39) nonsense probably null
IGL01399:Cntn1 APN 15 92,203,025 (GRCm39) missense probably damaging 1.00
IGL01714:Cntn1 APN 15 92,151,870 (GRCm39) nonsense probably null
IGL02052:Cntn1 APN 15 92,189,584 (GRCm39) missense possibly damaging 0.95
IGL02342:Cntn1 APN 15 92,143,898 (GRCm39) missense probably benign 0.01
IGL02507:Cntn1 APN 15 92,148,860 (GRCm39) missense possibly damaging 0.92
IGL02511:Cntn1 APN 15 92,114,266 (GRCm39) start gained probably benign
IGL02702:Cntn1 APN 15 92,189,482 (GRCm39) splice site probably benign
IGL02927:Cntn1 APN 15 92,189,561 (GRCm39) missense probably benign 0.12
IGL02948:Cntn1 APN 15 92,143,891 (GRCm39) missense probably benign 0.01
R0035:Cntn1 UTSW 15 92,129,969 (GRCm39) splice site probably benign
R0084:Cntn1 UTSW 15 92,215,798 (GRCm39) missense probably benign 0.01
R0346:Cntn1 UTSW 15 92,129,968 (GRCm39) splice site probably benign
R0634:Cntn1 UTSW 15 92,212,444 (GRCm39) nonsense probably null
R1348:Cntn1 UTSW 15 92,212,544 (GRCm39) missense probably damaging 1.00
R1613:Cntn1 UTSW 15 92,143,871 (GRCm39) missense possibly damaging 0.60
R1793:Cntn1 UTSW 15 92,189,552 (GRCm39) missense possibly damaging 0.92
R1815:Cntn1 UTSW 15 92,148,829 (GRCm39) missense probably benign 0.00
R1851:Cntn1 UTSW 15 92,203,021 (GRCm39) missense probably damaging 1.00
R1852:Cntn1 UTSW 15 92,203,021 (GRCm39) missense probably damaging 1.00
R2068:Cntn1 UTSW 15 92,215,943 (GRCm39) missense possibly damaging 0.82
R2269:Cntn1 UTSW 15 92,192,863 (GRCm39) splice site probably benign
R4394:Cntn1 UTSW 15 92,189,645 (GRCm39) missense probably damaging 1.00
R4667:Cntn1 UTSW 15 92,192,960 (GRCm39) missense probably damaging 1.00
R4771:Cntn1 UTSW 15 92,202,972 (GRCm39) missense possibly damaging 0.82
R4944:Cntn1 UTSW 15 92,126,549 (GRCm39) missense probably damaging 1.00
R5044:Cntn1 UTSW 15 92,140,876 (GRCm39) missense probably damaging 1.00
R5218:Cntn1 UTSW 15 92,237,430 (GRCm39) missense unknown
R5314:Cntn1 UTSW 15 92,192,892 (GRCm39) missense probably benign 0.01
R5445:Cntn1 UTSW 15 92,192,958 (GRCm39) missense probably damaging 1.00
R5518:Cntn1 UTSW 15 92,212,534 (GRCm39) missense probably benign 0.00
R6849:Cntn1 UTSW 15 92,203,127 (GRCm39) missense probably damaging 0.99
R7035:Cntn1 UTSW 15 92,212,392 (GRCm39) missense probably benign 0.04
R7070:Cntn1 UTSW 15 92,151,917 (GRCm39) missense probably damaging 1.00
R7287:Cntn1 UTSW 15 92,143,833 (GRCm39) splice site probably null
R7311:Cntn1 UTSW 15 92,130,156 (GRCm39) critical splice donor site probably null
R7401:Cntn1 UTSW 15 92,215,870 (GRCm39) missense probably benign
R7484:Cntn1 UTSW 15 92,151,922 (GRCm39) missense probably benign 0.00
R7492:Cntn1 UTSW 15 92,212,423 (GRCm39) missense probably benign
R7617:Cntn1 UTSW 15 92,143,970 (GRCm39) missense probably damaging 1.00
R7644:Cntn1 UTSW 15 92,207,890 (GRCm39) missense probably benign 0.14
R7878:Cntn1 UTSW 15 92,192,934 (GRCm39) missense probably damaging 1.00
R8354:Cntn1 UTSW 15 92,130,130 (GRCm39) missense probably benign
R8454:Cntn1 UTSW 15 92,130,130 (GRCm39) missense probably benign
R8465:Cntn1 UTSW 15 92,237,404 (GRCm39) frame shift probably null
R8757:Cntn1 UTSW 15 92,153,801 (GRCm39) missense possibly damaging 0.90
R8759:Cntn1 UTSW 15 92,153,801 (GRCm39) missense possibly damaging 0.90
R8767:Cntn1 UTSW 15 92,132,347 (GRCm39) missense probably damaging 1.00
R8768:Cntn1 UTSW 15 92,132,347 (GRCm39) missense probably damaging 1.00
R8885:Cntn1 UTSW 15 92,159,380 (GRCm39) missense probably benign 0.00
R8972:Cntn1 UTSW 15 92,150,278 (GRCm39) missense probably benign 0.18
R8993:Cntn1 UTSW 15 92,132,347 (GRCm39) missense probably damaging 1.00
R8995:Cntn1 UTSW 15 92,132,347 (GRCm39) missense probably damaging 1.00
R8997:Cntn1 UTSW 15 92,132,347 (GRCm39) missense probably damaging 1.00
R9151:Cntn1 UTSW 15 92,140,864 (GRCm39) missense probably damaging 1.00
R9438:Cntn1 UTSW 15 92,144,024 (GRCm39) critical splice donor site probably null
R9493:Cntn1 UTSW 15 92,189,644 (GRCm39) missense probably damaging 1.00
Z1177:Cntn1 UTSW 15 92,207,851 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTGGCTTCTGAATGAATTTCCTG -3'
(R):5'- TCCAAACACTTCCTAGGGTGG -3'

Sequencing Primer
(F):5'- CCTGTATTTATCACCATGGATAAGCG -3'
(R):5'- TTCCTAGGGTGGAAGCAATG -3'
Posted On 2018-10-18