Incidental Mutation 'R3944:Cntn4'
ID 307591
Institutional Source Beutler Lab
Gene Symbol Cntn4
Ensembl Gene ENSMUSG00000064293
Gene Name contactin 4
Synonyms BIG-2A, Axcam
MMRRC Submission 040925-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.313) question?
Stock # R3944 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 105654621-106676271 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 106595375 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 497 (N497K)
Ref Sequence ENSEMBL: ENSMUSP00000108883 (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
AA Change: N497K

PolyPhen 2 Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000108883
Gene: ENSMUSG00000064293
AA Change: N497K

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: ENSMUST00000132395
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.7%
Validation Efficiency 100% (61/61)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik G T 12: 71,211,320 (GRCm39) E685* probably null Het
2700049A03Rik A T 12: 71,211,321 (GRCm39) E685V possibly damaging Het
6430548M08Rik T C 8: 120,879,241 (GRCm39) L213P probably damaging Het
Akap12 A G 10: 4,307,347 (GRCm39) K1491E probably benign Het
Akr1c12 T A 13: 4,329,339 (GRCm39) H6L probably benign Het
Ankrd50 C T 3: 38,506,645 (GRCm39) C251Y probably benign Het
Bltp1 A G 3: 37,084,210 (GRCm39) I3876V possibly damaging Het
Bltp2 T A 11: 78,160,350 (GRCm39) L603* probably null Het
Calu T C 6: 29,361,710 (GRCm39) S125P possibly damaging Het
Cdh10 A G 15: 18,964,335 (GRCm39) T166A probably benign Het
Clip1 T C 5: 123,755,892 (GRCm39) probably benign Het
Cspg4 T A 9: 56,793,407 (GRCm39) C381S probably damaging Het
Cyp1a2 T C 9: 57,589,151 (GRCm39) N221S probably benign Het
Dnaaf5 C T 5: 139,138,679 (GRCm39) probably benign Het
Dnah7b A G 1: 46,176,645 (GRCm39) D755G probably damaging Het
Dscam A T 16: 96,622,197 (GRCm39) V418E probably damaging Het
Eefsec T A 6: 88,275,076 (GRCm39) H296L probably benign Het
Elmo3 T C 8: 106,035,852 (GRCm39) probably null Het
Gcm1 C T 9: 77,967,098 (GRCm39) Q106* probably null Het
Gnl1 G T 17: 36,299,413 (GRCm39) G528V probably benign Het
Gpat4 G A 8: 23,670,171 (GRCm39) P286L probably damaging Het
H2-T23 A G 17: 36,341,535 (GRCm39) V312A probably benign Het
Hectd4 C A 5: 121,441,588 (GRCm39) probably benign Het
Hoxa7 T A 6: 52,193,606 (GRCm39) probably benign Het
Ifnlr1 T A 4: 135,428,539 (GRCm39) V122E probably damaging Het
Kcnt2 T C 1: 140,512,025 (GRCm39) M1036T probably damaging Het
Khdc1b G T 1: 21,455,030 (GRCm39) K96N probably damaging Het
Kif19a A T 11: 114,677,561 (GRCm39) Y578F probably benign Het
Krt4 G A 15: 101,829,685 (GRCm39) T281M probably benign Het
Lyl1 A C 8: 85,430,631 (GRCm39) T178P probably damaging Het
Marchf6 A G 15: 31,488,960 (GRCm39) V317A probably benign Het
Mmp1b G A 9: 7,384,708 (GRCm39) T280I possibly damaging Het
Mpi T C 9: 57,452,536 (GRCm39) D332G probably damaging Het
Naip6 T C 13: 100,431,247 (GRCm39) T1197A probably benign Het
Ntng2 G A 2: 29,094,289 (GRCm39) L361F probably benign Het
Obscn A T 11: 59,023,373 (GRCm39) I668N probably damaging Het
Or52x1 A T 7: 104,853,162 (GRCm39) C129* probably null Het
Or8k40 A G 2: 86,584,525 (GRCm39) S186P probably benign Het
Pabpc1l A G 2: 163,884,247 (GRCm39) E328G probably damaging Het
Pan3 A T 5: 147,387,540 (GRCm39) N170Y probably damaging Het
Prdm2 C T 4: 142,858,385 (GRCm39) R1635Q possibly damaging Het
Rassf6 G T 5: 90,752,185 (GRCm39) Q258K possibly damaging Het
Ribc2 A G 15: 85,019,451 (GRCm39) M78V probably benign Het
Rp9 A C 9: 22,361,154 (GRCm39) H44Q probably damaging Het
Skint5 T A 4: 113,799,950 (GRCm39) H73L probably damaging Het
Slc6a12 A T 6: 121,331,239 (GRCm39) probably null Het
Smg6 G A 11: 74,820,367 (GRCm39) G213R probably damaging Het
Spout1 A G 2: 30,064,148 (GRCm39) V372A probably benign Het
Svep1 T A 4: 58,084,807 (GRCm39) probably null Het
Tab1 T C 15: 80,037,941 (GRCm39) L258P probably damaging Het
Tbl3 A G 17: 24,919,682 (GRCm39) S791P possibly damaging Het
Tcof1 C A 18: 60,955,909 (GRCm39) D927Y probably damaging Het
Tmem59l A G 8: 70,939,951 (GRCm39) L6S unknown Het
Topaz1 T C 9: 122,579,669 (GRCm39) S860P possibly damaging Het
Vill T C 9: 118,897,499 (GRCm39) I258T probably benign Het
Vmn1r204 G A 13: 22,741,014 (GRCm39) R215H probably benign Het
Vmn2r106 A T 17: 20,487,913 (GRCm39) F829I probably damaging Het
Vmn2r14 A T 5: 109,363,930 (GRCm39) I662N probably damaging Het
Vmn2r58 A T 7: 41,513,885 (GRCm39) F253I probably benign Het
Vps8 A T 16: 21,288,873 (GRCm39) N411Y probably damaging Het
Zfp932 T A 5: 110,157,820 (GRCm39) V506E probably benign 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
R1199:Cntn4 UTSW 6 106,330,558 (GRCm39) splice site probably benign
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
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'- CGAGGCTGTCAAATGATGTAAC -3'
(R):5'- CGATGCTGAAATAAGATAGCCTTTC -3'

Sequencing Primer
(F):5'- AGTTTCTCACGAGATAAACATCAC -3'
(R):5'- GCCTTTCAATCATATTCATTACCAAC -3'
Posted On 2015-04-17