Incidental Mutation 'R1906:Cntn4'
ID 214369
Institutional Source Beutler Lab
Gene Symbol Cntn4
Ensembl Gene ENSMUSG00000064293
Gene Name contactin 4
Synonyms BIG-2A, Axcam
MMRRC Submission 039925-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.313) question?
Stock # R1906 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 105654621-106676271 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 106330607 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 75 (F75S)
Ref Sequence ENSEMBL: ENSMUSP00000078385 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079416] [ENSMUST00000089208] [ENSMUST00000113258] [ENSMUST00000113260] [ENSMUST00000113261] [ENSMUST00000113264]
AlphaFold Q69Z26
Predicted Effect probably benign
Transcript: ENSMUST00000079416
AA Change: F75S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000078385
Gene: ENSMUSG00000064293
AA Change: F75S

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
AA Change: F75S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000086616
Gene: ENSMUSG00000064293
AA Change: F75S

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: F75S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108883
Gene: ENSMUSG00000064293
AA Change: F75S

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
AA Change: F75S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108885
Gene: ENSMUSG00000064293
AA Change: F75S

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
AA Change: F75S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108886
Gene: ENSMUSG00000064293
AA Change: F75S

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
AA Change: F75S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108889
Gene: ENSMUSG00000064293
AA Change: F75S

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
Coding Region Coverage
  • 1x: 97.3%
  • 3x: 96.7%
  • 10x: 94.9%
  • 20x: 91.5%
Validation Efficiency
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aass G A 6: 23,072,984 (GRCm39) T923I probably benign Het
Abhd13 T A 8: 10,038,170 (GRCm39) C256S probably benign Het
Adamts5 C T 16: 85,665,573 (GRCm39) W576* probably null Het
Adnp A T 2: 168,024,287 (GRCm39) S1003T probably benign Het
AI987944 C T 7: 41,024,550 (GRCm39) R146Q probably benign Het
Apol6 G T 15: 76,935,060 (GRCm39) V110F probably damaging Het
Arhgap27 A G 11: 103,223,751 (GRCm39) F651L probably damaging Het
Atm T C 9: 53,417,868 (GRCm39) D813G probably damaging Het
Casd1 T A 6: 4,641,979 (GRCm39) I752N probably damaging Het
Cdr2 A G 7: 120,581,224 (GRCm39) Y18H probably damaging Het
Col20a1 G A 2: 180,640,490 (GRCm39) R549H probably benign Het
Col28a1 A T 6: 7,999,644 (GRCm39) N1024K probably benign Het
Dnah10 T A 5: 124,878,048 (GRCm39) V2654D probably damaging Het
Dnph1 A T 17: 46,807,787 (GRCm39) I18F probably damaging Het
Dsn1 G A 2: 156,838,163 (GRCm39) R334W probably damaging Het
Egf T A 3: 129,518,873 (GRCm39) K325N probably benign Het
Eps15 T G 4: 109,181,398 (GRCm39) S311A possibly damaging Het
Fmo3 G T 1: 162,794,475 (GRCm39) D198E probably damaging Het
Folh1 C G 7: 86,391,374 (GRCm39) probably null Het
Foxn1 A G 11: 78,262,636 (GRCm39) probably null Het
Gm10604 T G 4: 11,979,989 (GRCm39) D105A unknown Het
Gpx8 A G 13: 113,182,110 (GRCm39) C108R probably damaging Het
Herc2 A T 7: 55,764,612 (GRCm39) I1013L probably benign Het
Hyal4 T G 6: 24,756,110 (GRCm39) N109K probably damaging Het
Il22ra1 T G 4: 135,478,544 (GRCm39) C538W probably damaging Het
Ints13 A T 6: 146,453,868 (GRCm39) probably null Het
Krt75 T A 15: 101,481,801 (GRCm39) T156S possibly damaging Het
Lama2 A C 10: 26,932,523 (GRCm39) probably null Het
Lifr G T 15: 7,217,612 (GRCm39) V847L probably damaging Het
Lmf1 T A 17: 25,831,309 (GRCm39) I185N probably damaging Het
Mast1 G A 8: 85,642,895 (GRCm39) R967C probably damaging Het
Ms4a15 T C 19: 10,960,644 (GRCm39) I94V probably benign Het
Mycbpap A T 11: 94,396,447 (GRCm39) M131K probably benign Het
Ncor1 A T 11: 62,240,211 (GRCm39) M920K possibly damaging Het
Neb A G 2: 52,198,538 (GRCm39) Y437H probably damaging Het
Npy5r A T 8: 67,134,125 (GRCm39) W223R probably damaging Het
Or10ak11 G A 4: 118,687,467 (GRCm39) H56Y probably damaging Het
Or10x4 C A 1: 174,218,730 (GRCm39) L32M probably damaging Het
Or4c114 A G 2: 88,905,414 (GRCm39) V7A possibly damaging Het
Or6c6c T G 10: 129,541,365 (GRCm39) V206G probably benign Het
Polg T C 7: 79,110,070 (GRCm39) K353E probably damaging Het
Proz C G 8: 13,123,686 (GRCm39) probably null Het
Pus7 T C 5: 23,983,209 (GRCm39) D86G probably damaging Het
Rhpn1 T C 15: 75,583,673 (GRCm39) V386A probably benign Het
Rigi T C 4: 40,206,054 (GRCm39) K846R probably benign Het
Sptbn4 A G 7: 27,090,856 (GRCm39) probably null Het
Srp68 A T 11: 116,141,587 (GRCm39) I424N probably damaging Het
Stard9 A G 2: 120,526,908 (GRCm39) E1055G probably benign Het
Taf4b A G 18: 14,955,159 (GRCm39) I571V probably benign Het
Tas2r107 T C 6: 131,636,951 (GRCm39) M33V probably benign Het
Thap12 T C 7: 98,365,947 (GRCm39) L705P probably damaging Het
Tom1 T C 8: 75,778,218 (GRCm39) V100A probably damaging Het
Tox3 A G 8: 90,975,057 (GRCm39) probably benign Het
Vmn2r82 A G 10: 79,232,344 (GRCm39) N781S probably damaging Het
Vwa5b1 A T 4: 138,327,547 (GRCm39) V343E possibly damaging Het
Zbbx A G 3: 74,979,047 (GRCm39) Y467H probably damaging Het
Zbtb46 G A 2: 181,065,632 (GRCm39) R173W probably damaging Het
Zfp112 A G 7: 23,821,720 (GRCm39) D20G probably benign Het
Zfp777 A C 6: 48,018,995 (GRCm39) M313R probably 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
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
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'- TTACTATAGAAGACAGCCCTCTCCC -3'
(R):5'- CTCAAAGAAACATTGGAGGTGC -3'

Sequencing Primer
(F):5'- GATGTCACCATTGCTGAATAGAC -3'
(R):5'- CATTGGAGGTGCAATATAATGACTAC -3'
Posted On 2014-07-14