Incidental Mutation 'R9376:Cntn4'
ID 709617
Institutional Source Beutler Lab
Gene Symbol Cntn4
Ensembl Gene ENSMUSG00000064293
Gene Name contactin 4
Synonyms BIG-2A, Axcam
MMRRC Submission
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.318) question?
Stock # R9376 (G1)
Quality Score 225.009
Status Not validated
Chromosome 6
Chromosomal Location 105654621-106676271 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 106639591 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 574 (Y574H)
Ref Sequence ENSEMBL: ENSMUSP00000108886 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000079416] [ENSMUST00000089208] [ENSMUST00000113260] [ENSMUST00000113261] [ENSMUST00000113264]
AlphaFold Q69Z26
PDB Structure Immunoglobulin domains 1-4 of mouse CNTN4 [X-RAY DIFFRACTION]
PTPRG CNTN4 complex [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000079416
AA Change: Y574H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000078385
Gene: ENSMUSG00000064293
AA Change: Y574H

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 damaging
Transcript: ENSMUST00000089208
AA Change: Y574H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000086616
Gene: ENSMUSG00000064293
AA Change: Y574H

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 damaging
Transcript: ENSMUST00000113260
AA Change: Y574H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108885
Gene: ENSMUSG00000064293
AA Change: Y574H

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 damaging
Transcript: ENSMUST00000113261
AA Change: Y574H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108886
Gene: ENSMUSG00000064293
AA Change: Y574H

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 damaging
Transcript: ENSMUST00000113264
AA Change: Y574H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108889
Gene: ENSMUSG00000064293
AA Change: Y574H

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
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.] 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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 T A 7: 119,893,438 (GRCm39) L1296H probably damaging Het
Abcb4 A T 5: 9,008,988 (GRCm39) D1215V probably damaging Het
Ache A C 5: 137,289,025 (GRCm39) I244L probably benign Het
Ankrd13d A T 19: 4,332,250 (GRCm39) V58D probably damaging Het
Ano3 A G 2: 110,496,782 (GRCm39) L789S probably damaging Het
Atp2a3 T C 11: 72,863,290 (GRCm39) V129A probably damaging Het
Cldn11 T C 3: 31,217,410 (GRCm39) S193P possibly damaging Het
Clpb A T 7: 101,360,625 (GRCm39) R218S probably benign Het
Cntln A G 4: 84,875,258 (GRCm39) S231G probably benign Het
Col6a3 C T 1: 90,709,523 (GRCm39) R2498H unknown Het
Ctdnep1 T C 11: 69,875,594 (GRCm39) V108A probably damaging Het
Cyp2c67 A T 19: 39,627,178 (GRCm39) N217K probably damaging Het
Dao T A 5: 114,147,901 (GRCm39) M1K probably null Het
Dchs1 A G 7: 105,414,981 (GRCm39) probably null Het
Dennd4a A T 9: 64,819,974 (GRCm39) I1809L probably benign Het
Dnah7a T A 1: 53,568,058 (GRCm39) probably null Het
Epn1 A T 7: 5,086,720 (GRCm39) probably benign Het
Erich1 A G 8: 14,080,719 (GRCm39) S267P probably damaging Het
Gm17732 G T 18: 62,795,936 (GRCm39) V41L probably damaging Het
Gpaa1 C A 15: 76,218,826 (GRCm39) T556K possibly damaging Het
Gpr65 T A 12: 98,241,523 (GRCm39) S59T probably damaging Het
Hydin T C 8: 111,124,695 (GRCm39) V568A possibly damaging Het
Ifi205 T C 1: 173,854,221 (GRCm39) D144G probably benign Het
Itga1 T C 13: 115,107,112 (GRCm39) H993R probably benign Het
Itgax T C 7: 127,747,935 (GRCm39) L1075P possibly damaging Het
Itpr1 T A 6: 108,326,638 (GRCm39) V120E probably damaging Het
Kdm3b T C 18: 34,970,718 (GRCm39) S1762P probably damaging Het
Krt80 T A 15: 101,247,978 (GRCm39) T221S unknown Het
Lama2 T C 10: 26,994,620 (GRCm39) D1763G probably benign Het
Lrp5 T C 19: 3,670,286 (GRCm39) D606G probably benign Het
Map6d1 T C 16: 20,059,933 (GRCm39) D44G probably benign Het
Mtmr11 T A 3: 96,072,372 (GRCm39) I282K probably benign Het
Nalcn G A 14: 123,515,713 (GRCm39) T1696M possibly damaging Het
Nup214 T C 2: 31,924,244 (GRCm39) V1591A probably benign Het
Oas1f C A 5: 120,986,243 (GRCm39) Y65* probably null Het
Or1x6 T A 11: 50,939,662 (GRCm39) C243S probably damaging Het
Or2t43 T A 11: 58,457,683 (GRCm39) T163S possibly damaging Het
Or2t46 T C 11: 58,472,636 (GRCm39) V322A probably benign Het
Or51f1e A T 7: 102,746,971 (GRCm39) T8S probably benign Het
Or5p58 A T 7: 107,694,471 (GRCm39) I102K possibly damaging Het
Palld C T 8: 61,969,691 (GRCm39) R1211H unknown Het
Pigyl A G 9: 22,069,324 (GRCm39) I12V probably benign Het
Pno1 A T 11: 17,158,791 (GRCm39) D202E probably benign Het
Ppp5c A T 7: 16,743,849 (GRCm39) M195K probably damaging Het
Prrc2a A T 17: 35,369,598 (GRCm39) F1905Y possibly damaging Het
Ptpn11 C A 5: 121,282,681 (GRCm39) D435Y probably damaging Het
Rbm33 A G 5: 28,544,164 (GRCm39) Y140C probably damaging Het
Runx1t1 A G 4: 13,865,225 (GRCm39) E339G possibly damaging Het
Scube3 G T 17: 28,383,670 (GRCm39) K480N possibly damaging Het
Sephs1 T A 2: 4,910,469 (GRCm39) M313K probably benign Het
Tcaim T C 9: 122,655,995 (GRCm39) W304R probably damaging Het
Terf2ip C T 8: 112,738,514 (GRCm39) T134I probably damaging Het
Terf2ip A G 8: 112,744,528 (GRCm39) T282A probably benign Het
Tnfrsf18 G T 4: 156,112,448 (GRCm39) A102S probably benign Het
Trim10 A T 17: 37,184,168 (GRCm39) I254F probably benign Het
Triqk A G 4: 12,962,987 (GRCm39) T9A probably benign Het
Tshz2 G A 2: 169,726,013 (GRCm39) S203N probably benign Het
Zc3h13 G A 14: 75,561,128 (GRCm39) V573I unknown Het
Zfhx4 A G 3: 5,306,833 (GRCm39) K20E probably damaging Het
Zfhx4 A G 3: 5,465,395 (GRCm39) D1876G 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
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
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'- TTCTAATAGCCGTGGCATGC -3'
(R):5'- GACTGTTAATCACTATGCACTATGG -3'

Sequencing Primer
(F):5'- CGTGGCATGCATCACTAATG -3'
(R):5'- CACTATGCACTATGGTTAACTTATGC -3'
Posted On 2022-04-18