Incidental Mutation 'R8454:Cntn1'
ID 654956
Institutional Source Beutler Lab
Gene Symbol Cntn1
Ensembl Gene ENSMUSG00000055022
Gene Name contactin 1
Synonyms F3cam, usl, CNTN
MMRRC Submission 067831-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8454 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 91949034-92239834 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 92130130 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 126 (T126A)
Ref Sequence ENSEMBL: ENSMUSP00000000109 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000109] [ENSMUST00000068378] [ENSMUST00000169825]
AlphaFold P12960
Predicted Effect probably benign
Transcript: ENSMUST00000000109
AA Change: T126A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000000109
Gene: ENSMUSG00000055022
AA Change: T126A

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 benign
Transcript: ENSMUST00000068378
AA Change: T126A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000067842
Gene: ENSMUSG00000055022
AA Change: T126A

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 benign
Transcript: ENSMUST00000169825
AA Change: T126A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000133063
Gene: ENSMUSG00000055022
AA Change: T126A

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: 99.7%
  • 20x: 98.9%
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. 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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc10 C A 17: 46,635,103 (GRCm39) G300V possibly damaging Het
Adgrg7 C G 16: 56,616,045 (GRCm39) probably benign Het
Agt G A 8: 125,290,842 (GRCm39) T155M probably benign Het
Atp8b3 A G 10: 80,361,633 (GRCm39) V763A probably benign Het
Btn1a1 C A 13: 23,648,420 (GRCm39) V138L probably benign Het
Cd163 A T 6: 124,305,924 (GRCm39) N1109I probably benign Het
Cideb T A 14: 55,992,598 (GRCm39) Q106L possibly damaging Het
Dnai3 T C 3: 145,802,982 (GRCm39) K70E probably damaging Het
Elfn1 T C 5: 139,957,226 (GRCm39) Y77H probably damaging Het
Eml3 A G 19: 8,912,358 (GRCm39) H386R probably damaging Het
Fbxo21 A G 5: 118,133,479 (GRCm39) D413G probably damaging Het
Fkbp8 T A 8: 70,984,413 (GRCm39) probably null Het
Fzd1 T C 5: 4,807,336 (GRCm39) Q82R probably benign Het
Gast T C 11: 100,227,394 (GRCm39) L29P probably benign Het
Glb1l2 C A 9: 26,717,713 (GRCm39) probably benign Het
Gm1110 C G 9: 26,794,576 (GRCm39) Q483H probably benign Het
Gm1110 T A 9: 26,794,577 (GRCm39) Q483L probably benign Het
Gpc6 T C 14: 117,163,391 (GRCm39) L15P probably damaging Het
Hagh C A 17: 25,076,536 (GRCm39) S161* probably null Het
Hrh1 A G 6: 114,457,814 (GRCm39) D365G probably benign Het
Ighv1-36 A T 12: 114,843,560 (GRCm39) M100K probably damaging Het
Itgb8 A T 12: 119,134,513 (GRCm39) V518D probably benign Het
Krt82 T C 15: 101,450,238 (GRCm39) Y486C probably damaging Het
Lmbr1l A G 15: 98,810,357 (GRCm39) S85P probably damaging Het
Met A G 6: 17,491,768 (GRCm39) S177G probably damaging Het
Myl9 T A 2: 156,623,048 (GRCm39) I162N possibly damaging Het
Npat T A 9: 53,478,251 (GRCm39) N973K possibly damaging Het
Or5p68 A T 7: 107,945,889 (GRCm39) C100S probably damaging Het
Pcdhga12 A T 18: 37,901,190 (GRCm39) D674V possibly damaging Het
Phtf1 T A 3: 103,911,765 (GRCm39) N702K probably damaging Het
Plaa A T 4: 94,457,714 (GRCm39) I752N probably damaging Het
Pnpla2 T C 7: 141,038,011 (GRCm39) C194R probably damaging Het
Rnaseh2a T C 8: 85,691,776 (GRCm39) N133S probably benign Het
Rps6ka1 T A 4: 133,575,864 (GRCm39) Q685L probably benign Het
Ryr1 C A 7: 28,715,142 (GRCm39) G4661C unknown Het
Samd13 T A 3: 146,352,157 (GRCm39) M65L probably benign Het
Sdr42e2 T A 7: 120,430,403 (GRCm39) V420E possibly damaging Het
Sec22c A G 9: 121,524,721 (GRCm39) S21P probably damaging Het
Sh3d19 C A 3: 86,014,329 (GRCm39) T431K probably benign Het
Sin3b A G 8: 73,468,108 (GRCm39) M277V probably benign Het
Sis T C 3: 72,854,834 (GRCm39) T468A possibly damaging Het
Slitrk3 T C 3: 72,956,513 (GRCm39) N753S probably benign Het
Slitrk6 C A 14: 110,989,478 (GRCm39) L76F probably damaging Het
Stk3 C T 15: 34,876,870 (GRCm39) A478T probably damaging Het
Styxl2 A T 1: 165,935,702 (GRCm39) N165K probably damaging Het
Sugp1 C A 8: 70,524,247 (GRCm39) Y617* probably null Het
Tinag T C 9: 76,938,977 (GRCm39) D167G probably damaging Het
Tk2 A G 8: 104,967,746 (GRCm39) probably null Het
Tmem209 A T 6: 30,489,308 (GRCm39) V514D probably damaging Het
Tmprss9 A G 10: 80,723,320 (GRCm39) H260R probably benign Het
Tnfrsf14 T A 4: 155,011,112 (GRCm39) Y83F possibly damaging Het
Tnfrsf8 A T 4: 145,014,553 (GRCm39) D285E probably benign Het
Togaram2 C G 17: 72,004,873 (GRCm39) A310G probably benign Het
Trpv3 A G 11: 73,182,448 (GRCm39) Y544C probably damaging Het
Ttl T A 2: 128,908,104 (GRCm39) V13D probably damaging Het
Usp40 A T 1: 87,908,694 (GRCm39) D602E probably benign Het
Vamp5 A G 6: 72,347,376 (GRCm39) probably benign Het
Vmn2r65 T A 7: 84,589,402 (GRCm39) H838L possibly damaging Het
Vps35l T A 7: 118,391,795 (GRCm39) F493Y probably benign Het
Zfp960 T A 17: 17,308,461 (GRCm39) Y392N probably benign 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
R6885:Cntn1 UTSW 15 92,140,980 (GRCm39) critical splice donor site probably null
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
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'- CGACAGTTCCCAGACTTACG -3'
(R):5'- TCACTGCGTTGGTTGCAATG -3'

Sequencing Primer
(F):5'- CCCAGACTTACGAGTTTCAGTGTAAC -3'
(R):5'- CAAGAGTAGTCGGCATGTTTCAACTC -3'
Posted On 2020-10-20