Incidental Mutation 'R1199:Cntn4'
ID 101204
Institutional Source Beutler Lab
Gene Symbol Cntn4
Ensembl Gene ENSMUSG00000064293
Gene Name contactin 4
Synonyms BIG-2A, Axcam
MMRRC Submission 039269-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.318) question?
Stock # R1199 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 105654621-106676271 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to C at 106330558 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000108889 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079416] [ENSMUST00000089208] [ENSMUST00000113258] [ENSMUST00000113260] [ENSMUST00000113261] [ENSMUST00000113264]
AlphaFold Q69Z26
Predicted Effect probably benign
Transcript: ENSMUST00000079416
SMART Domains Protein: ENSMUSP00000078385
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
IG 504 594 9.55e-10 SMART
FN3 597 683 1.54e-11 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000089208
SMART Domains Protein: ENSMUSP00000086616
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
IG 504 594 9.55e-10 SMART
FN3 597 683 1.54e-11 SMART
FN3 700 786 8.39e0 SMART
FN3 801 886 1.33e-6 SMART
FN3 901 981 9.85e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113258
SMART Domains Protein: ENSMUSP00000108883
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113260
SMART Domains Protein: ENSMUSP00000108885
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
IG 504 594 9.55e-10 SMART
FN3 597 683 1.54e-11 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113261
SMART Domains Protein: ENSMUSP00000108886
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
IG 504 594 9.55e-10 SMART
FN3 597 683 1.54e-11 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000113264
SMART Domains Protein: ENSMUSP00000108889
Gene: ENSMUSG00000064293

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IGc2 41 107 2.32e-8 SMART
IG 129 215 3.4e-6 SMART
IGc2 238 302 8.76e-18 SMART
IGc2 328 391 2.91e-14 SMART
IGc2 420 484 1.58e-10 SMART
IG 504 594 9.55e-10 SMART
FN3 597 683 1.54e-11 SMART
FN3 700 786 8.39e0 SMART
FN3 801 886 1.33e-6 SMART
FN3 901 981 9.85e-1 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125904
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 91.5%
Validation Efficiency 96% (55/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit aberrant projection of olfactory axons to multiple glomeruli in the olfactory bulb. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700102P08Rik A T 9: 108,270,676 (GRCm39) H80L possibly damaging Het
A1bg A T 15: 60,791,484 (GRCm39) probably null Het
Aco2 C T 15: 81,779,394 (GRCm39) S33L probably damaging Het
Agrn T A 4: 156,256,756 (GRCm39) Y1283F probably benign Het
Akap6 T C 12: 52,842,973 (GRCm39) V107A probably damaging Het
Amph G A 13: 19,326,198 (GRCm39) V643M probably damaging Het
Btnl9 A T 11: 49,071,574 (GRCm39) V83E probably damaging Het
Camk2a T A 18: 61,085,396 (GRCm39) C131* probably null Het
Ccdc14 C T 16: 34,544,198 (GRCm39) T852M probably damaging Het
Cp T G 3: 20,031,316 (GRCm39) S585R probably damaging Het
Cpt1b G A 15: 89,303,213 (GRCm39) A614V probably benign Het
Crygn T C 5: 24,956,146 (GRCm39) Y153C probably damaging Het
Dennd1a A T 2: 37,851,728 (GRCm39) D53E probably damaging Het
Deptor T C 15: 55,115,406 (GRCm39) C357R probably benign Het
Dnajc28 C A 16: 91,415,530 (GRCm39) probably benign Het
Eml6 G A 11: 29,705,044 (GRCm39) A1500V possibly damaging Het
Fgd5 T A 6: 91,963,959 (GRCm39) L64Q possibly damaging Het
Fgfbp1 A G 5: 44,136,939 (GRCm39) Y118H probably damaging Het
Ftcd G A 10: 76,415,653 (GRCm39) R135H probably damaging Het
Gm5174 A T 10: 86,493,189 (GRCm39) noncoding transcript Het
Gpr37l1 A T 1: 135,094,710 (GRCm39) L178Q probably damaging Het
Gtf2ird1 A G 5: 134,439,918 (GRCm39) V104A possibly damaging Het
Irs1 T A 1: 82,267,347 (GRCm39) S290C probably damaging Het
Kel C T 6: 41,665,525 (GRCm39) V532I possibly damaging Het
Kif1c A G 11: 70,599,427 (GRCm39) E442G possibly damaging Het
Klhdc10 T A 6: 30,449,493 (GRCm39) V185D probably damaging Het
Lpp C T 16: 24,500,610 (GRCm39) R141C probably damaging Het
Or52a5 A T 7: 103,427,192 (GRCm39) M120K probably damaging Het
Or5m13 A G 2: 85,748,379 (GRCm39) I37V probably benign Het
Pcnx2 G T 8: 126,614,053 (GRCm39) P466H possibly damaging Het
Pcsk1 A T 13: 75,244,532 (GRCm39) probably benign Het
Pkd2l2 T C 18: 34,571,269 (GRCm39) probably null Het
Pomt1 A G 2: 32,140,504 (GRCm39) N454S probably benign Het
Samhd1 A T 2: 156,951,381 (GRCm39) I452N probably damaging Het
Sez6 A G 11: 77,844,711 (GRCm39) Q178R probably benign Het
Slc25a44 A G 3: 88,328,293 (GRCm39) V66A probably damaging Het
Slc46a2 T C 4: 59,914,189 (GRCm39) T245A probably benign Het
Slc4a4 G A 5: 89,363,653 (GRCm39) probably null Het
Spata6 T A 4: 111,656,342 (GRCm39) C329S possibly damaging Het
Srrm2 A T 17: 24,036,725 (GRCm39) probably benign Het
Stard9 C A 2: 120,504,117 (GRCm39) S221R probably damaging Het
Svil T A 18: 5,059,217 (GRCm39) probably benign Het
Tenm3 G T 8: 48,688,617 (GRCm39) S2323R probably damaging Het
Tsc1 G A 2: 28,555,638 (GRCm39) R245Q probably damaging Het
Ttn A G 2: 76,739,100 (GRCm39) V3813A probably benign Het
Ttn G A 2: 76,780,388 (GRCm39) T1121M possibly damaging Het
Ush2a G A 1: 188,491,992 (GRCm39) V3094I probably benign Het
Vcan A G 13: 89,827,913 (GRCm39) probably null Het
Vmn1r189 A T 13: 22,286,828 (GRCm39) L3Q probably damaging Het
Vmn1r60 A C 7: 5,547,971 (GRCm39) V43G probably damaging Het
Vmn2r110 A G 17: 20,803,525 (GRCm39) I350T probably benign Het
Vmn2r86 T A 10: 130,284,443 (GRCm39) probably benign Het
Xrn1 A G 9: 95,863,814 (GRCm39) probably benign Het
Zfp251 C T 15: 76,738,436 (GRCm39) R219Q possibly damaging Het
Other mutations in Cntn4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00092:Cntn4 APN 6 106,483,186 (GRCm39) missense probably damaging 1.00
IGL00725:Cntn4 APN 6 106,639,616 (GRCm39) missense probably damaging 1.00
IGL01062:Cntn4 APN 6 106,595,239 (GRCm39) splice site probably benign
IGL01432:Cntn4 APN 6 106,655,295 (GRCm39) splice site probably benign
IGL01585:Cntn4 APN 6 106,595,289 (GRCm39) nonsense probably null
IGL01710:Cntn4 APN 6 106,527,392 (GRCm39) missense possibly damaging 0.87
IGL01870:Cntn4 APN 6 106,466,676 (GRCm39) missense possibly damaging 0.95
IGL01933:Cntn4 APN 6 106,671,345 (GRCm39) missense probably damaging 0.99
IGL01937:Cntn4 APN 6 106,414,865 (GRCm39) missense probably damaging 1.00
IGL01945:Cntn4 APN 6 106,414,865 (GRCm39) missense probably damaging 1.00
IGL02007:Cntn4 APN 6 106,632,490 (GRCm39) missense probably benign 0.03
IGL02506:Cntn4 APN 6 106,595,349 (GRCm39) missense probably benign 0.24
IGL02561:Cntn4 APN 6 106,500,470 (GRCm39) missense probably damaging 1.00
IGL03080:Cntn4 APN 6 106,632,500 (GRCm39) missense probably damaging 1.00
IGL03338:Cntn4 APN 6 106,632,550 (GRCm39) missense probably damaging 0.98
IGL03097:Cntn4 UTSW 6 106,330,673 (GRCm39) missense probably benign 0.10
LCD18:Cntn4 UTSW 6 106,530,901 (GRCm39) intron probably benign
R0083:Cntn4 UTSW 6 106,502,330 (GRCm39) missense possibly damaging 0.79
R0098:Cntn4 UTSW 6 106,595,385 (GRCm39) splice site probably benign
R0501:Cntn4 UTSW 6 106,595,296 (GRCm39) missense probably damaging 1.00
R0626:Cntn4 UTSW 6 106,639,539 (GRCm39) missense probably benign 0.07
R0633:Cntn4 UTSW 6 106,656,209 (GRCm39) splice site probably null
R0730:Cntn4 UTSW 6 106,527,447 (GRCm39) missense probably damaging 1.00
R0849:Cntn4 UTSW 6 106,644,418 (GRCm39) missense probably damaging 1.00
R0883:Cntn4 UTSW 6 106,644,501 (GRCm39) splice site probably benign
R0926:Cntn4 UTSW 6 106,632,542 (GRCm39) missense probably benign 0.21
R1293:Cntn4 UTSW 6 106,330,685 (GRCm39) missense probably benign 0.00
R1296:Cntn4 UTSW 6 106,486,363 (GRCm39) missense probably damaging 1.00
R1344:Cntn4 UTSW 6 106,321,831 (GRCm39) splice site probably null
R1418:Cntn4 UTSW 6 106,321,831 (GRCm39) splice site probably null
R1660:Cntn4 UTSW 6 106,656,258 (GRCm39) missense probably benign 0.35
R1751:Cntn4 UTSW 6 106,595,371 (GRCm39) critical splice donor site probably null
R1883:Cntn4 UTSW 6 106,656,353 (GRCm39) missense probably benign 0.01
R1884:Cntn4 UTSW 6 106,656,353 (GRCm39) missense probably benign 0.01
R1899:Cntn4 UTSW 6 106,652,774 (GRCm39) missense probably benign 0.21
R1906:Cntn4 UTSW 6 106,330,607 (GRCm39) missense probably benign 0.00
R2048:Cntn4 UTSW 6 106,414,825 (GRCm39) splice site probably benign
R2113:Cntn4 UTSW 6 106,466,658 (GRCm39) missense probably damaging 1.00
R3177:Cntn4 UTSW 6 106,414,925 (GRCm39) critical splice donor site probably null
R3277:Cntn4 UTSW 6 106,414,925 (GRCm39) critical splice donor site probably null
R3944:Cntn4 UTSW 6 106,595,375 (GRCm39) missense probably benign 0.10
R4401:Cntn4 UTSW 6 106,466,625 (GRCm39) missense possibly damaging 0.94
R4540:Cntn4 UTSW 6 106,652,709 (GRCm39) missense probably damaging 1.00
R4688:Cntn4 UTSW 6 106,414,910 (GRCm39) missense probably damaging 1.00
R4697:Cntn4 UTSW 6 106,502,446 (GRCm39) missense probably damaging 1.00
R4810:Cntn4 UTSW 6 106,632,572 (GRCm39) missense probably benign 0.04
R4816:Cntn4 UTSW 6 106,527,458 (GRCm39) missense probably benign
R4873:Cntn4 UTSW 6 106,414,874 (GRCm39) missense possibly damaging 0.61
R4875:Cntn4 UTSW 6 106,414,874 (GRCm39) missense possibly damaging 0.61
R4953:Cntn4 UTSW 6 106,502,379 (GRCm39) missense probably benign 0.01
R5288:Cntn4 UTSW 6 106,158,765 (GRCm39) missense possibly damaging 0.60
R5336:Cntn4 UTSW 6 106,639,595 (GRCm39) missense possibly damaging 0.72
R5386:Cntn4 UTSW 6 106,158,765 (GRCm39) missense possibly damaging 0.60
R5477:Cntn4 UTSW 6 106,650,911 (GRCm39) missense possibly damaging 0.88
R5514:Cntn4 UTSW 6 106,649,844 (GRCm39) missense probably damaging 1.00
R5668:Cntn4 UTSW 6 106,656,397 (GRCm39) splice site silent
R6334:Cntn4 UTSW 6 106,321,747 (GRCm39) missense probably benign
R6334:Cntn4 UTSW 6 106,483,153 (GRCm39) missense probably benign 0.29
R6904:Cntn4 UTSW 6 106,674,544 (GRCm39) missense probably benign 0.03
R6985:Cntn4 UTSW 6 106,656,378 (GRCm39) missense probably benign 0.03
R7246:Cntn4 UTSW 6 106,483,180 (GRCm39) missense probably damaging 1.00
R7282:Cntn4 UTSW 6 106,502,421 (GRCm39) missense probably damaging 0.99
R7585:Cntn4 UTSW 6 106,466,572 (GRCm39) missense probably damaging 1.00
R7667:Cntn4 UTSW 6 106,656,856 (GRCm39) missense possibly damaging 0.83
R7781:Cntn4 UTSW 6 106,500,575 (GRCm39) missense probably damaging 1.00
R7882:Cntn4 UTSW 6 106,330,684 (GRCm39) missense probably benign
R8081:Cntn4 UTSW 6 106,651,568 (GRCm39) missense possibly damaging 0.95
R8105:Cntn4 UTSW 6 106,330,567 (GRCm39) missense probably damaging 1.00
R8221:Cntn4 UTSW 6 106,486,471 (GRCm39) missense probably benign 0.17
R8910:Cntn4 UTSW 6 106,632,497 (GRCm39) missense probably benign 0.10
R8911:Cntn4 UTSW 6 106,330,743 (GRCm39) critical splice donor site probably null
R8916:Cntn4 UTSW 6 106,652,915 (GRCm39) missense probably damaging 0.99
R9249:Cntn4 UTSW 6 106,466,722 (GRCm39) missense possibly damaging 0.95
R9376:Cntn4 UTSW 6 106,639,591 (GRCm39) missense probably damaging 1.00
R9616:Cntn4 UTSW 6 106,674,525 (GRCm39) nonsense probably null
R9767:Cntn4 UTSW 6 106,655,395 (GRCm39) missense probably benign 0.40
Z1176:Cntn4 UTSW 6 106,500,524 (GRCm39) missense probably benign 0.00
Z1176:Cntn4 UTSW 6 106,486,425 (GRCm39) missense probably benign 0.28
Z1177:Cntn4 UTSW 6 106,639,579 (GRCm39) missense probably damaging 1.00
Z1177:Cntn4 UTSW 6 106,527,386 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATTTACTATAGAAGACAGCCCTCTCCCC -3'
(R):5'- TCAGGCTCTATGAAACATACCTCTTTGC -3'

Sequencing Primer
(F):5'- AGCCCTCTCCCCACAAG -3'
(R):5'- CTGTCAGAAGGTACTGTTTGTAAAG -3'
Posted On 2014-01-15