Mutagenetix > Incidental Mutation

Incidental Mutation 'R2507:Cdh6'

251403

Institutional Source

Beutler Lab

Gene Symbol

Cdh6

Ensembl Gene

ENSMUSG00000039385

Gene Name

cadherin 6

Synonyms

K-cadherin, cad6

MMRRC Submission

040413-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.272) question?

Stock #

R2507 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

13028787-13173761 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13041447 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 539 (I539T)

Ref Sequence

ENSEMBL: ENSMUSP00000037113 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000036439]

AlphaFold

P97326

PDB Structure

Crystal structure of cadherin-6 EC12 W4A [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000036439
AA Change: I539T

PolyPhen 2 Score 0.103 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000037113
Gene: ENSMUSG00000039385
AA Change: I539T

Domain	Start	End	E-Value	Type
CA	76	157	7e-15	SMART
CA	181	266	9.06e-32	SMART
CA	290	382	1.14e-19	SMART
CA	405	486	8.81e-21	SMART
CA	509	596	2.82e-10	SMART
transmembrane domain	614	636	N/A	INTRINSIC
Pfam:Cadherin_C	639	783	5.6e-57	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.7%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the cadherin family of calcium-dependent glycoproteins that mediate cell adhesion and regulate many morphogenetic events during development. The encoded preproprotein is further processed to generate a mature protein. Mice lacking the encoded protein exhibit delay in mesenchyme-to-epithelial conversion and a loss of nephrons. Multiple distinct genes of the cadherin family, including this gene, are found on chromosome 15. [provided by RefSeq, Oct 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit delayed mesenchyme to epithelial conversion and loss of nephrons. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N01Rik	A	G	10: 21,497,681 (GRCm39)		probably benign	Het
4930535I16Rik	G	A	4: 123,811,740 (GRCm39)		probably benign	Het
Akr1b1	C	T	6: 34,286,999 (GRCm39)	E186K	probably damaging	Het
Apc	A	T	18: 34,449,590 (GRCm39)	N2128I	possibly damaging	Het
Api5	T	C	2: 94,260,162 (GRCm39)	I31M	probably damaging	Het
Armcx4	T	G	X: 133,596,128 (GRCm39)	V2012G	possibly damaging	Het
Aurka	T	C	2: 172,212,365 (GRCm39)	E4G	probably benign	Het
B4galt5	T	A	2: 167,148,558 (GRCm39)	M187L	probably benign	Het
Bsn	T	C	9: 107,993,313 (GRCm39)	D813G	probably damaging	Het
Bub1	A	T	2: 127,643,343 (GRCm39)	D1000E	probably benign	Het
Cacna1f	T	G	X: 7,492,687 (GRCm39)		probably null	Het
Cdhr3	T	C	12: 33,088,914 (GRCm39)	D756G	probably benign	Het
Cenph	A	T	13: 100,907,744 (GRCm39)	D85E	probably benign	Het
Chd9	C	T	8: 91,760,615 (GRCm39)	P2120L	probably benign	Het
Clec2h	A	G	6: 128,650,945 (GRCm39)	N75S	probably benign	Het
Cnga1	C	T	5: 72,776,404 (GRCm39)	V20I	possibly damaging	Het
Cox4i1	T	A	8: 121,400,029 (GRCm39)	V51E	possibly damaging	Het
Cpne3	A	T	4: 19,553,871 (GRCm39)	N53K	probably damaging	Het
Cpt1b	A	G	15: 89,303,301 (GRCm39)	F585L	probably benign	Het
Daam1	G	A	12: 72,021,997 (GRCm39)	D732N	probably damaging	Het
Dner	A	T	1: 84,560,801 (GRCm39)	C115S	probably damaging	Het
Dop1a	T	A	9: 86,395,170 (GRCm39)	F759Y	probably damaging	Het
Dst	T	C	1: 34,050,990 (GRCm39)	Y29H	probably damaging	Het
Dst	T	C	1: 34,227,498 (GRCm39)	V1875A	possibly damaging	Het
Duox1	A	G	2: 122,163,619 (GRCm39)	D817G	probably benign	Het
Emc2	A	T	15: 43,375,094 (GRCm39)		probably null	Het
Erich3	A	T	3: 154,404,296 (GRCm39)	E51V	probably null	Het
Exoc2	A	G	13: 31,066,348 (GRCm39)	Y443H	possibly damaging	Het
Fbf1	T	C	11: 116,046,252 (GRCm39)	R200G	probably benign	Het
Fdxr	G	A	11: 115,162,806 (GRCm39)	T100I	probably damaging	Het
Galnt11	C	G	5: 25,452,610 (GRCm39)	P41A	probably damaging	Het
Galnt4	A	G	10: 98,945,148 (GRCm39)	K291R	possibly damaging	Het
Gm12695	T	A	4: 96,642,426 (GRCm39)	E301V	probably damaging	Het
Gopc	C	T	10: 52,229,422 (GRCm39)		probably null	Het
Gria1	A	T	11: 57,180,146 (GRCm39)	T699S	probably null	Het
Gsr	T	G	8: 34,170,316 (GRCm39)	D200E	probably benign	Het
Ikzf2	G	A	1: 69,578,447 (GRCm39)	A282V	probably benign	Het
Irak2	T	C	6: 113,624,639 (GRCm39)	I45T	probably damaging	Het
Irx1	T	C	13: 72,107,939 (GRCm39)	K248E	probably damaging	Het
Kcns3	A	C	12: 11,142,087 (GRCm39)	V204G	possibly damaging	Het
Lmo1	C	A	7: 108,739,848 (GRCm39)	M91I	probably damaging	Het
Map3k21	A	G	8: 126,666,677 (GRCm39)	D623G	possibly damaging	Het
Map4	A	G	9: 109,866,551 (GRCm39)		probably benign	Het
Mark3	T	A	12: 111,593,676 (GRCm39)	V236E	probably damaging	Het
Med23	A	G	10: 24,786,711 (GRCm39)	D939G	probably damaging	Het
Mrgpra9	A	G	7: 46,885,242 (GRCm39)	C142R	possibly damaging	Het
N4bp2	T	A	5: 65,947,404 (GRCm39)	D11E	probably benign	Het
Ntng2	T	C	2: 29,097,531 (GRCm39)	N310S	probably damaging	Het
Or10ak7	T	C	4: 118,791,122 (GRCm39)	M308V	probably benign	Het
Or6b3	A	G	1: 92,439,100 (GRCm39)	S217P	probably damaging	Het
Pcolce	A	G	5: 137,605,313 (GRCm39)	V260A	possibly damaging	Het
Pds5b	C	A	5: 150,679,893 (GRCm39)	T533K	possibly damaging	Het
Pecr	A	G	1: 72,301,135 (GRCm39)	Y268H	probably benign	Het
Phax	T	A	18: 56,719,956 (GRCm39)	F299Y	probably damaging	Het
Phip	T	C	9: 82,797,392 (GRCm39)	H537R	possibly damaging	Het
Pramel32	T	A	4: 88,547,448 (GRCm39)	K161N	possibly damaging	Het
Prpf39	T	A	12: 65,104,589 (GRCm39)	F551L	probably benign	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Ralgapa1	G	A	12: 55,764,986 (GRCm39)	P889S	probably damaging	Het
Rpap1	A	G	2: 119,610,535 (GRCm39)		probably null	Het
Rufy3	T	C	5: 88,797,757 (GRCm39)	S645P	probably damaging	Het
Samd1	CGAGGAGGAGGAGGAGGAGGA	CGAGGAGGAGGAGGAGGA	8: 84,725,625 (GRCm39)		probably benign	Het
Spata7	G	T	12: 98,624,709 (GRCm39)	A172S	probably benign	Het
Stk35	A	G	2: 129,643,435 (GRCm39)	T140A	probably damaging	Het
Thop1	T	G	10: 80,906,098 (GRCm39)	M1R	probably null	Het
Tlr1	T	C	5: 65,082,639 (GRCm39)	Y646C	probably damaging	Het
Tpp2	A	G	1: 44,040,609 (GRCm39)	Y290C	probably benign	Het
Tpr	A	G	1: 150,268,695 (GRCm39)	M1V	probably null	Het
Trim6	T	C	7: 103,877,392 (GRCm39)	F161L	probably damaging	Het
Ubash3b	T	C	9: 41,068,650 (GRCm39)	K25E	possibly damaging	Het
Unc45b	G	A	11: 82,830,963 (GRCm39)		probably null	Het
Unc80	A	G	1: 66,651,266 (GRCm39)	N1537S	possibly damaging	Het
Usb1	T	C	8: 96,069,752 (GRCm39)	F100S	probably damaging	Het
Vmn1r17	C	A	6: 57,338,244 (GRCm39)	L40F	probably damaging	Het
Vmn1r233	A	T	17: 21,214,110 (GRCm39)	M280K	probably benign	Het
Zfp37	A	T	4: 62,109,493 (GRCm39)	C524S	probably damaging	Het
Zfp426	T	C	9: 20,381,727 (GRCm39)	K420R	probably benign	Het

Other mutations in Cdh6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00560:Cdh6	APN	15	13,034,445 (GRCm39)	nonsense	probably null
IGL00675:Cdh6	APN	15	13,041,525 (GRCm39)	missense	possibly damaging	0.80
IGL01063:Cdh6	APN	15	13,064,581 (GRCm39)	missense	probably damaging	1.00
IGL01335:Cdh6	APN	15	13,051,395 (GRCm39)	missense	probably benign	0.40
IGL01351:Cdh6	APN	15	13,034,326 (GRCm39)	missense	possibly damaging	0.55
IGL02010:Cdh6	APN	15	13,034,276 (GRCm39)	utr 3 prime	probably benign
IGL02428:Cdh6	APN	15	13,064,516 (GRCm39)	missense	possibly damaging	0.94
PIT4651001:Cdh6	UTSW	15	13,044,805 (GRCm39)	missense	possibly damaging	0.69
R0124:Cdh6	UTSW	15	13,034,410 (GRCm39)	missense	probably damaging	1.00
R0256:Cdh6	UTSW	15	13,053,868 (GRCm39)	splice site	probably benign
R0696:Cdh6	UTSW	15	13,051,418 (GRCm39)	missense	probably benign	0.36
R1017:Cdh6	UTSW	15	13,051,562 (GRCm39)	missense	probably benign	0.06
R1240:Cdh6	UTSW	15	13,057,541 (GRCm39)	missense	possibly damaging	0.48
R1444:Cdh6	UTSW	15	13,091,924 (GRCm39)	missense	probably benign	0.00
R2008:Cdh6	UTSW	15	13,051,562 (GRCm39)	missense	possibly damaging	0.74
R2050:Cdh6	UTSW	15	13,057,587 (GRCm39)	missense	probably benign
R3082:Cdh6	UTSW	15	13,044,838 (GRCm39)	missense	probably damaging	1.00
R3083:Cdh6	UTSW	15	13,044,838 (GRCm39)	missense	probably damaging	1.00
R3903:Cdh6	UTSW	15	13,042,661 (GRCm39)	missense	probably benign	0.39
R4591:Cdh6	UTSW	15	13,051,572 (GRCm39)	missense	possibly damaging	0.69
R4859:Cdh6	UTSW	15	13,051,418 (GRCm39)	missense	probably benign	0.36
R4898:Cdh6	UTSW	15	13,034,774 (GRCm39)	missense	probably damaging	0.99
R5242:Cdh6	UTSW	15	13,064,497 (GRCm39)	missense	probably benign	0.05
R5313:Cdh6	UTSW	15	13,034,723 (GRCm39)	missense	probably damaging	1.00
R5545:Cdh6	UTSW	15	13,041,235 (GRCm39)	missense	probably damaging	1.00
R6360:Cdh6	UTSW	15	13,041,546 (GRCm39)	missense	possibly damaging	0.82
R6650:Cdh6	UTSW	15	13,051,487 (GRCm39)	missense	probably benign	0.11
R6830:Cdh6	UTSW	15	13,044,860 (GRCm39)	missense	probably benign	0.01
R7369:Cdh6	UTSW	15	13,042,724 (GRCm39)	missense	probably damaging	0.99
R7506:Cdh6	UTSW	15	13,034,396 (GRCm39)	missense	probably damaging	1.00
R8121:Cdh6	UTSW	15	13,044,757 (GRCm39)	missense	probably damaging	1.00
R8801:Cdh6	UTSW	15	13,044,847 (GRCm39)	missense	probably damaging	1.00
R8961:Cdh6	UTSW	15	13,041,447 (GRCm39)	missense	probably benign	0.12
R9218:Cdh6	UTSW	15	13,057,556 (GRCm39)	missense	probably null	0.37
R9258:Cdh6	UTSW	15	13,064,462 (GRCm39)	missense	probably damaging	1.00
R9511:Cdh6	UTSW	15	13,034,677 (GRCm39)	missense	probably damaging	1.00
R9608:Cdh6	UTSW	15	13,064,621 (GRCm39)	missense	probably damaging	1.00
R9636:Cdh6	UTSW	15	13,057,655 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TGTCCGAAATGACCACAGG -3'
(R):5'- CTGTGAGAACCACTTTCGGG -3'

Sequencing Primer
(F):5'- CAGGAGATAGGTGCTCATCTC -3'
(R):5'- GCCCTGAGCCTTTGTGACAG -3'

Posted On

2014-12-04