Mutagenetix > Incidental Mutation

Incidental Mutation 'R8105:Cntn4'

630687

Institutional Source

Beutler Lab

Gene Symbol

Cntn4

Ensembl Gene

ENSMUSG00000064293

Gene Name

contactin 4

Synonyms

BIG-2A, Axcam

MMRRC Submission

067536-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.318) question?

Stock #

R8105 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

105654621-106676271 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 106330567 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 62 (W62R)

Ref Sequence

ENSEMBL: ENSMUSP00000108886 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000079416] [ENSMUST00000089208] [ENSMUST00000113258] [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: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000078385
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000086616
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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: ENSMUST00000113258
AA Change: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108883
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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 damaging
Transcript: ENSMUST00000113260
AA Change: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108885
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108886
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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: W62R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000108889
Gene: ENSMUSG00000064293
AA Change: W62R

Domain	Start	End	E-Value	Type
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

Meta Mutation Damage Score

0.9433

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

100% (29/29)

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: 28 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arid1b	G	A	17: 5,341,518 (GRCm39)	A941T	possibly damaging	Het
Calb1	A	T	4: 15,900,767 (GRCm39)		probably null	Het
Cc2d1b	T	C	4: 108,485,130 (GRCm39)	S518P	possibly damaging	Het
Clpsl2	G	A	17: 28,769,702 (GRCm39)	G55R	probably damaging	Het
Cltc	C	T	11: 86,598,438 (GRCm39)	V975I	probably damaging	Het
Crot	A	G	5: 9,027,505 (GRCm39)	Y276H	probably damaging	Het
Dnah5	T	C	15: 28,372,548 (GRCm39)	V2933A	probably benign	Het
Evl	C	T	12: 108,647,783 (GRCm39)	R295*	probably null	Het
Fhod1	T	C	8: 106,063,847 (GRCm39)	T253A	unknown	Het
Fndc3b	G	A	3: 27,524,374 (GRCm39)	T462I	probably benign	Het
Folh1	A	T	7: 86,395,354 (GRCm39)	N359K	probably damaging	Het
Gmppa	T	C	1: 75,413,641 (GRCm39)	V34A	possibly damaging	Het
Ift140	A	G	17: 25,255,949 (GRCm39)	T484A	probably benign	Het
Lrrtm2	T	C	18: 35,346,510 (GRCm39)	E264G	probably damaging	Het
Luc7l2	T	C	6: 38,569,588 (GRCm39)	F182S	probably benign	Het
Ly9	G	C	1: 171,432,890 (GRCm39)		probably null	Het
Meox2	C	T	12: 37,159,061 (GRCm39)	H78Y	possibly damaging	Het
Mynn	G	A	3: 30,665,628 (GRCm39)	C420Y	possibly damaging	Het
Or52e18	C	G	7: 104,609,629 (GRCm39)	M103I	probably benign	Het
Rfx1	C	G	8: 84,814,505 (GRCm39)	A358G	possibly damaging	Het
Rnf151	G	A	17: 24,935,400 (GRCm39)	T177I	probably benign	Het
Spef2	T	G	15: 9,682,748 (GRCm39)	N578H	probably benign	Het
Stpg2	A	G	3: 138,948,925 (GRCm39)	I240M	probably damaging	Het
Tln1	C	T	4: 43,538,231 (GRCm39)	V1824I	probably benign	Het
Ugt3a1	T	A	15: 9,306,476 (GRCm39)	F208L	probably benign	Het
Vldlr	C	T	19: 27,216,204 (GRCm39)	Q342*	probably null	Het
Vmn1r14	T	A	6: 57,211,245 (GRCm39)	F274L	probably benign	Het
Xrcc6	T	C	15: 81,915,352 (GRCm39)	L435P	probably damaging	Het

Other mutations in Cntn4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- TCTCCCCACAAGTACTTAAGATGTC -3'
(R):5'- CTCAAAGAAACATTGGAGGTGC -3'

Sequencing Primer
(F):5'- GATGTCACCATTGCTGAATAGAC -3'
(R):5'- CATTGGAGGTGCAATATAATGACTAC -3'

Posted On

2020-06-30