Mutagenetix > Incidental Mutation

Incidental Mutation 'R4944:Cdh2'

383380

Institutional Source

Beutler Lab

Gene Symbol

Cdh2

Ensembl Gene

ENSMUSG00000024304

Gene Name

cadherin 2

Synonyms

N-CAD, N-cadherin, Ncad

MMRRC Submission

042541-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4944 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

16721934-16942303 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 16783466 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 88 (Y88H)

Ref Sequence

ENSEMBL: ENSMUSP00000025166 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025166] [ENSMUST00000115850]

AlphaFold

P15116

PDB Structure

STRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS [X-RAY DIFFRACTION]
STRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS [X-RAY DIFFRACTION]
STRUCTURAL BASIS OF CELL-CELL ADHESION BY CADHERINS [X-RAY DIFFRACTION]
N-CADHERIN, TWO-DOMAIN FRAGMENT [X-RAY DIFFRACTION]
Solution Structure of Neural Cadherin Prodomain [SOLUTION NMR]
Crystal structure of N-cadherin domains EC12 [X-RAY DIFFRACTION]
Crystal structure of mouse N-cadherin ectodomain [X-RAY DIFFRACTION]
Crystal structure of mouse N-cadherin EC1-2 A78SI92M [X-RAY DIFFRACTION]
Crystal structure of mouse N-cadherin EC1-2 with AA insertion between residues 2 and 3 [X-RAY DIFFRACTION]
Crystal structure of mouse N-cadherin EC1-2 W2F [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000025166
AA Change: Y88H

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000025166
Gene: ENSMUSG00000024304
AA Change: Y88H

Domain	Start	End	E-Value	Type
low complexity region	5	21	N/A	INTRINSIC
Cadherin_pro	31	123	5.77e-34	SMART
low complexity region	129	141	N/A	INTRINSIC
CA	182	265	3.37e-17	SMART
CA	289	380	2.15e-33	SMART
CA	403	496	4.38e-16	SMART
CA	519	603	2.27e-23	SMART
CA	623	708	5.54e-2	SMART
transmembrane domain	724	746	N/A	INTRINSIC
Pfam:Cadherin_C	753	903	6.3e-54	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000115850
AA Change: Y31H

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000111516
Gene: ENSMUSG00000024304
AA Change: Y31H

Domain	Start	End	E-Value	Type
Cadherin_pro	1	66	3.44e-9	SMART
low complexity region	72	84	N/A	INTRINSIC
CA	125	208	3.37e-17	SMART
CA	232	323	2.15e-33	SMART
CA	346	439	4.38e-16	SMART
CA	462	546	2.27e-23	SMART
CA	566	651	5.54e-2	SMART
transmembrane domain	667	689	N/A	INTRINSIC
Pfam:Cadherin_C	690	847	2.5e-57	PFAM

Meta Mutation Damage Score

0.4926

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

100% (67/67)

MGI Phenotype

FUNCTION: This gene encodes a member of the cadherin family of calcium-dependent glycoproteins that mediate cell adhesion. The encoded preproprotein undergoes proteolytic processing to generate a mature protein. Mice lacking the encoded protein exhibit severe developmental defects resulting in embryonic death. [provided by RefSeq, Oct 2015]
PHENOTYPE: Homozygous mutation of this gene results in death by E10. Mutant embryos exhibit several developmental abnormalities such as growth retardation, an enlarged heart, distended pericardial sacs, abnormal heart tube, wavy neural tube, irregular somite shape,and abnormal embryo turning. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb4	G	A	5: 8,984,327 (GRCm39)		probably null	Het
Angptl7	C	G	4: 148,584,534 (GRCm39)	Q71H	probably damaging	Het
Arhgap30	A	T	1: 171,229,822 (GRCm39)	N176Y	probably damaging	Het
Armc9	T	A	1: 86,202,256 (GRCm39)	S805T	probably damaging	Het
Atxn1	T	G	13: 45,720,407 (GRCm39)	H496P	probably damaging	Het
Cabin1	C	T	10: 75,557,197 (GRCm39)	G1147D	probably damaging	Het
Cabin1	A	G	10: 75,575,255 (GRCm39)	S597P	probably damaging	Het
Catsperd	T	C	17: 56,969,744 (GRCm39)	S613P	probably damaging	Het
Cntn1	C	A	15: 92,126,549 (GRCm39)	P47Q	probably damaging	Het
Col11a2	T	C	17: 34,261,164 (GRCm39)	L38P	possibly damaging	Het
Col5a2	T	G	1: 45,415,855 (GRCm39)	I1431L	possibly damaging	Het
Csmd1	C	T	8: 16,048,772 (GRCm39)	G2310D	probably damaging	Het
Dhcr7	T	A	7: 143,391,528 (GRCm39)	I39N	probably damaging	Het
Dnajc13	C	T	9: 104,044,586 (GRCm39)		probably benign	Het
Drgx	G	T	14: 32,330,206 (GRCm39)	Q136H	probably damaging	Het
Folr2	T	C	7: 101,489,497 (GRCm39)		probably null	Het
Galnt11	T	C	5: 25,470,336 (GRCm39)	I595T	probably damaging	Het
Gp5	G	A	16: 30,128,326 (GRCm39)	A116V	possibly damaging	Het
Gpn3	T	C	5: 122,520,303 (GRCm39)		probably benign	Het
Gprin3	T	C	6: 59,331,644 (GRCm39)	N221S	probably benign	Het
Hfm1	T	C	5: 107,022,079 (GRCm39)	E989G	possibly damaging	Het
Ints1	T	C	5: 139,743,847 (GRCm39)		probably null	Het
Josd2	T	C	7: 44,120,592 (GRCm39)	S110P	probably damaging	Het
Kat14	C	A	2: 144,217,873 (GRCm39)	T123K	probably damaging	Het
Lamtor1	C	T	7: 101,558,971 (GRCm39)	T48I	probably damaging	Het
Lrrc24	A	G	15: 76,602,546 (GRCm39)	L113P	probably damaging	Het
Lrrc37	T	C	11: 103,504,286 (GRCm39)	T2561A	possibly damaging	Het
Mog	T	C	17: 37,331,433 (GRCm39)	E89G	probably damaging	Het
Mon2	A	G	10: 122,874,364 (GRCm39)		probably null	Het
Mtx1	T	C	3: 89,121,205 (GRCm39)	Y143C	probably benign	Het
Nacad	T	C	11: 6,548,507 (GRCm39)	E1409G	possibly damaging	Het
Ndst3	T	C	3: 123,400,676 (GRCm39)	H410R	probably damaging	Het
Nkx6-2	T	C	7: 139,161,486 (GRCm39)	E233G	possibly damaging	Het
Oas1h	A	G	5: 121,000,846 (GRCm39)	E152G	probably damaging	Het
Or8g22	A	G	9: 38,958,158 (GRCm39)	S186P	probably damaging	Het
Ovgp1	T	C	3: 105,887,269 (GRCm39)	F222L	possibly damaging	Het
Pkhd1	T	C	1: 20,358,429 (GRCm39)	S2716G	probably null	Het
Pla2g4e	T	C	2: 120,001,718 (GRCm39)	T644A	probably benign	Het
Plxnd1	A	G	6: 115,932,726 (GRCm39)	I1918T	probably damaging	Het
Psmg1	A	T	16: 95,790,812 (GRCm39)		probably benign	Het
Ptprd	G	A	4: 76,047,136 (GRCm39)	R364C	probably damaging	Het
Rgs22	T	C	15: 36,026,088 (GRCm39)	I945V	possibly damaging	Het
Rgs7bp	T	C	13: 105,088,072 (GRCm39)	N234S	probably benign	Het
Rrp7a	T	C	15: 83,004,010 (GRCm39)		probably benign	Het
Scg2	T	A	1: 79,414,193 (GRCm39)	R177*	probably null	Het
Sema4c	C	A	1: 36,589,392 (GRCm39)	C578F	probably damaging	Het
Slc1a5	T	A	7: 16,531,668 (GRCm39)		probably benign	Het
Slc5a3	A	G	16: 91,875,571 (GRCm39)	T543A	possibly damaging	Het
Slx4ip	T	A	2: 136,888,687 (GRCm39)	F123I	probably benign	Het
Smtn	C	T	11: 3,472,916 (GRCm39)	R737H	probably damaging	Het
Stox2	A	G	8: 47,866,300 (GRCm39)	I14T	possibly damaging	Het
Stradb	T	C	1: 59,019,599 (GRCm39)	F43L	probably benign	Het
Szt2	T	C	4: 118,245,866 (GRCm39)	D1029G	probably benign	Het
Taar6	T	C	10: 23,860,613 (GRCm39)	Y311C	probably damaging	Het
Tcea3	A	T	4: 135,995,404 (GRCm39)	N249I	probably damaging	Het
Tecta	A	G	9: 42,241,573 (GRCm39)	M2134T	probably benign	Het
Tg	G	A	15: 66,636,186 (GRCm39)	G591D	probably damaging	Het
Tm4sf20	T	A	1: 82,746,084 (GRCm39)	I19F	probably benign	Het
Top2a	T	C	11: 98,888,676 (GRCm39)	K1262E	probably benign	Het
Ube2r2	A	G	4: 41,190,742 (GRCm39)		probably benign	Het
Usp29	T	C	7: 6,964,927 (GRCm39)	S257P	possibly damaging	Het
Usp40	T	C	1: 87,880,077 (GRCm39)	N1038S	probably benign	Het
Utp25	A	T	1: 192,797,262 (GRCm39)	M530K	probably damaging	Het
Vmn1r121	C	T	7: 20,831,538 (GRCm39)	E301K	probably benign	Het
Vmn2r49	T	A	7: 9,722,959 (GRCm39)	H105L	probably benign	Het
Zgrf1	C	T	3: 127,355,517 (GRCm39)	Q248*	probably null	Het

Other mutations in Cdh2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00517:Cdh2	APN	18	16,760,693 (GRCm39)	missense	possibly damaging	0.69
IGL01560:Cdh2	APN	18	16,783,495 (GRCm39)	missense	probably benign	0.01
IGL02028:Cdh2	APN	18	16,783,477 (GRCm39)	missense	probably benign	0.07
IGL02227:Cdh2	APN	18	16,762,643 (GRCm39)	missense	probably benign	0.01
IGL02229:Cdh2	APN	18	16,757,810 (GRCm39)	missense	probably benign
IGL02617:Cdh2	APN	18	16,760,661 (GRCm39)	missense	probably damaging	1.00
IGL02685:Cdh2	APN	18	16,779,557 (GRCm39)	missense	probably damaging	1.00
IGL02724:Cdh2	APN	18	16,762,537 (GRCm39)	missense	probably benign	0.29
R0111:Cdh2	UTSW	18	16,907,566 (GRCm39)	missense	probably benign
R0173:Cdh2	UTSW	18	16,783,314 (GRCm39)	splice site	probably benign
R0197:Cdh2	UTSW	18	16,762,633 (GRCm39)	missense	probably benign
R0563:Cdh2	UTSW	18	16,762,738 (GRCm39)	missense	possibly damaging	0.90
R0883:Cdh2	UTSW	18	16,762,633 (GRCm39)	missense	probably benign
R1083:Cdh2	UTSW	18	16,777,016 (GRCm39)	missense	possibly damaging	0.61
R1270:Cdh2	UTSW	18	16,760,614 (GRCm39)	splice site	probably benign
R1469:Cdh2	UTSW	18	16,757,324 (GRCm39)	missense	possibly damaging	0.92
R1469:Cdh2	UTSW	18	16,757,324 (GRCm39)	missense	possibly damaging	0.92
R1510:Cdh2	UTSW	18	16,781,651 (GRCm39)	missense	probably benign
R1875:Cdh2	UTSW	18	16,757,934 (GRCm39)	missense	probably benign
R2122:Cdh2	UTSW	18	16,907,600 (GRCm39)	missense	probably benign	0.01
R2194:Cdh2	UTSW	18	16,773,505 (GRCm39)	missense	probably damaging	1.00
R2254:Cdh2	UTSW	18	16,776,985 (GRCm39)	critical splice donor site	probably null
R4471:Cdh2	UTSW	18	16,907,533 (GRCm39)	splice site	probably null
R4501:Cdh2	UTSW	18	16,762,642 (GRCm39)	missense	possibly damaging	0.53
R4620:Cdh2	UTSW	18	16,781,665 (GRCm39)	missense	probably benign
R4832:Cdh2	UTSW	18	16,760,754 (GRCm39)	missense	probably benign	0.01
R4958:Cdh2	UTSW	18	16,760,622 (GRCm39)	splice site	probably null
R5160:Cdh2	UTSW	18	16,762,644 (GRCm39)	missense	probably damaging	0.99
R5190:Cdh2	UTSW	18	16,783,372 (GRCm39)	missense	possibly damaging	0.54
R5446:Cdh2	UTSW	18	16,779,684 (GRCm39)	missense	probably damaging	1.00
R5552:Cdh2	UTSW	18	16,773,520 (GRCm39)	missense	possibly damaging	0.88
R5699:Cdh2	UTSW	18	16,779,579 (GRCm39)	nonsense	probably null
R5912:Cdh2	UTSW	18	16,773,507 (GRCm39)	missense	possibly damaging	0.79
R5949:Cdh2	UTSW	18	16,734,687 (GRCm39)	missense	probably damaging	1.00
R6313:Cdh2	UTSW	18	16,907,579 (GRCm39)	missense	probably benign	0.00
R6633:Cdh2	UTSW	18	16,773,605 (GRCm39)	missense	probably benign	0.00
R7822:Cdh2	UTSW	18	16,757,341 (GRCm39)	missense	probably benign	0.24
R8022:Cdh2	UTSW	18	16,723,358 (GRCm39)	missense	probably damaging	1.00
R8142:Cdh2	UTSW	18	16,734,791 (GRCm39)	missense	probably benign	0.00
R8152:Cdh2	UTSW	18	16,762,576 (GRCm39)	missense	probably benign	0.02
R8188:Cdh2	UTSW	18	16,781,593 (GRCm39)	missense	probably damaging	1.00
R8461:Cdh2	UTSW	18	16,783,522 (GRCm39)	missense	probably benign	0.44
R8491:Cdh2	UTSW	18	16,757,775 (GRCm39)	critical splice donor site	probably null
R9246:Cdh2	UTSW	18	16,781,654 (GRCm39)	nonsense	probably null
R9477:Cdh2	UTSW	18	16,755,212 (GRCm39)	missense	probably damaging	1.00
R9530:Cdh2	UTSW	18	16,783,466 (GRCm39)	missense	probably damaging	0.99
R9581:Cdh2	UTSW	18	16,803,112 (GRCm39)	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- AATCAAGTCTCCAAAGCCAGATCTG -3'
(R):5'- GACATGCTCAGGAACTTGTGC -3'

Sequencing Primer
(F):5'- TTACAGCTACCTGCCACT -3'
(R):5'- AACAGTTTCTGTGAGTCCATGATGC -3'

Posted On

2016-04-27