Mutagenetix > Incidental Mutation

Incidental Mutation 'R4832:Cdh2'

372952

Institutional Source

Beutler Lab

Gene Symbol

Cdh2

Ensembl Gene

ENSMUSG00000024304

Gene Name

cadherin 2

Synonyms

N-CAD, N-cadherin, Ncad

MMRRC Submission

042448-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4832 (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 16760754 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 538 (S538P)

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 benign
Transcript: ENSMUST00000025166
AA Change: S538P

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000025166
Gene: ENSMUSG00000024304
AA Change: S538P

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 benign
Transcript: ENSMUST00000115850
AA Change: S481P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000111516
Gene: ENSMUSG00000024304
AA Change: S481P

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

0.1054

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.9%

Validation Efficiency

98% (106/108)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110032F04Rik	T	C	3: 68,777,597 (GRCm39)	V186A	possibly damaging	Het
1700088E04Rik	A	T	15: 79,019,409 (GRCm39)	M198K	probably damaging	Het
4933402J07Rik	A	G	8: 88,294,601 (GRCm39)	K84R	probably null	Het
Aamdc	T	C	7: 97,199,773 (GRCm39)		probably null	Het
Abcc9	A	G	6: 142,617,282 (GRCm39)	V594A	probably damaging	Het
Adamts13	G	A	2: 26,879,414 (GRCm39)	D656N	probably benign	Het
Adcy10	G	T	1: 165,334,213 (GRCm39)	C122F	probably damaging	Het
Adi1	A	G	12: 28,725,252 (GRCm39)	M1V	probably null	Het
Ahnak	G	A	19: 8,989,824 (GRCm39)		probably benign	Het
Akt1	G	T	12: 112,623,521 (GRCm39)	P313Q	probably damaging	Het
Ano3	A	T	2: 110,498,067 (GRCm39)	M758K	probably damaging	Het
Baz2a	T	A	10: 127,958,999 (GRCm39)	N1168K	probably benign	Het
Bbs10	A	G	10: 111,136,995 (GRCm39)	K703E	probably benign	Het
Bcap29	A	G	12: 31,674,202 (GRCm39)	I131T	probably benign	Het
Brd10	G	T	19: 29,694,616 (GRCm39)	L1626I	possibly damaging	Het
Btnl6	T	C	17: 34,732,966 (GRCm39)	D299G	possibly damaging	Het
Ccdc66	A	G	14: 27,222,524 (GRCm39)	I73T	probably benign	Het
Cfap54	T	A	10: 92,803,390 (GRCm39)	M1551L	probably benign	Het
Chd2	G	A	7: 73,151,873 (GRCm39)	A243V	probably damaging	Het
Cntnap1	T	A	11: 101,073,845 (GRCm39)	N665K	probably damaging	Het
Colgalt2	C	T	1: 152,360,749 (GRCm39)	T262I	possibly damaging	Het
Cyp24a1	T	C	2: 170,338,098 (GRCm39)	I149V	probably benign	Het
Cyp2a5	T	A	7: 26,534,970 (GRCm39)		probably null	Het
Dab2	A	G	15: 6,366,080 (GRCm39)		probably null	Het
Dnah17	T	A	11: 117,917,606 (GRCm39)	I4158F	probably damaging	Het
Dnm2	G	A	9: 21,385,975 (GRCm39)		probably null	Het
Dpp7	A	T	2: 25,242,398 (GRCm39)		probably benign	Het
Epha6	T	A	16: 59,780,776 (GRCm39)	I642F	probably damaging	Het
Erbb4	T	C	1: 68,369,397 (GRCm39)	S415G	probably benign	Het
Fancd2	A	G	6: 113,530,683 (GRCm39)	T439A	probably benign	Het
Fat1	G	A	8: 45,466,102 (GRCm39)	V1431M	possibly damaging	Het
Fhod3	G	A	18: 25,223,305 (GRCm39)	A884T	probably benign	Het
Fsip2	A	G	2: 82,820,515 (GRCm39)	D5416G	possibly damaging	Het
Gabarap	C	T	11: 69,882,678 (GRCm39)		probably benign	Het
Garre1	T	C	7: 33,938,333 (GRCm39)		probably benign	Het
Gm11544	C	T	11: 94,736,532 (GRCm39)		noncoding transcript	Het
Gnat2	A	C	3: 108,007,964 (GRCm39)	K304Q	probably benign	Het
Gpr141b	T	A	13: 19,913,840 (GRCm39)		noncoding transcript	Het
Gramd4	C	T	15: 86,019,057 (GRCm39)	A575V	probably benign	Het
Gtpbp10	G	A	5: 5,589,295 (GRCm39)	A274V	possibly damaging	Het
Gzmb	A	G	14: 56,497,679 (GRCm39)	I187T	probably damaging	Het
H2-M10.2	G	A	17: 36,595,219 (GRCm39)	T315I	probably damaging	Het
Haus5	A	T	7: 30,356,452 (GRCm39)	F524I	probably damaging	Het
Herc1	A	G	9: 66,403,253 (GRCm39)	S4391G	probably benign	Het
Herc2	T	A	7: 55,748,165 (GRCm39)	L511*	probably null	Het
Htt	T	A	5: 34,982,184 (GRCm39)	C923S	probably benign	Het
Idua	T	C	5: 108,817,247 (GRCm39)	S7P	probably benign	Het
Ighv16-1	A	T	12: 114,032,466 (GRCm39)	L112Q	probably damaging	Het
Igkv1-110	A	G	6: 68,248,185 (GRCm39)	K98R	probably benign	Het
Kif15	G	A	9: 122,831,191 (GRCm39)		probably null	Het
Leng9	C	A	7: 4,152,029 (GRCm39)	G216W	probably damaging	Het
Lrpprc	A	G	17: 85,014,584 (GRCm39)	L1306S	probably benign	Het
Lztfl1	C	A	9: 123,544,454 (GRCm39)	E20D	possibly damaging	Het
Maob	T	C	X: 16,582,662 (GRCm39)	T400A	probably benign	Het
Map3k4	C	T	17: 12,490,667 (GRCm39)	E255K	probably damaging	Het
Megf9	G	A	4: 70,452,665 (GRCm39)	T132M	probably damaging	Het
Mob4	T	C	1: 55,184,411 (GRCm39)		probably benign	Het
Mttp	G	A	3: 137,821,811 (GRCm39)	A252V	probably benign	Het
Mxi1	A	G	19: 53,358,745 (GRCm39)	D226G	probably damaging	Het
Myh14	A	G	7: 44,274,566 (GRCm39)	S1249P	probably benign	Het
Mylk	G	A	16: 34,742,737 (GRCm39)	G1083D	probably benign	Het
Mylk4	T	G	13: 32,905,960 (GRCm39)	I408L	probably benign	Het
Nbas	A	G	12: 13,533,740 (GRCm39)	S1792G	probably benign	Het
Nelfb	A	G	2: 25,099,981 (GRCm39)	V212A	probably damaging	Het
Nisch	T	C	14: 30,899,587 (GRCm39)		probably benign	Het
Nqo1	C	G	8: 108,115,477 (GRCm39)	D267H	probably benign	Het
Or8u10	C	A	2: 85,915,190 (GRCm39)	L310F	probably benign	Het
Pcid2	T	A	8: 13,135,425 (GRCm39)	I195F	probably damaging	Het
Pcnx2	A	T	8: 126,478,927 (GRCm39)	M2107K	probably damaging	Het
Pgd	A	T	4: 149,241,048 (GRCm39)		probably benign	Het
Prim2	T	C	1: 33,503,145 (GRCm39)	M430V	probably benign	Het
Prkaa1	A	G	15: 5,190,101 (GRCm39)	T40A	probably damaging	Het
Ptges	T	C	2: 30,793,232 (GRCm39)		probably benign	Het
Ptprn	T	C	1: 75,234,909 (GRCm39)	E226G	probably benign	Het
Rab14	A	G	2: 35,079,978 (GRCm39)	F55S	probably damaging	Het
Ralgps2	A	T	1: 156,684,637 (GRCm39)		probably benign	Het
Rgs11	C	T	17: 26,426,542 (GRCm39)	H258Y	probably benign	Het
Rhpn2	T	C	7: 35,075,774 (GRCm39)		probably null	Het
Rprd2	A	T	3: 95,681,483 (GRCm39)	V452E	probably damaging	Het
Scube3	C	A	17: 28,384,989 (GRCm39)	H646Q	probably damaging	Het
Selp	A	T	1: 163,953,909 (GRCm39)	I70F	probably damaging	Het
Septin2	A	G	1: 93,426,849 (GRCm39)	I153V	probably damaging	Het
Sh3rf3	G	A	10: 58,649,905 (GRCm39)	S170N	probably benign	Het
Skint4	A	T	4: 112,000,963 (GRCm39)	I353F	possibly damaging	Het
Slc16a12	A	G	19: 34,657,780 (GRCm39)	I41T	possibly damaging	Het
Snai2	T	C	16: 14,524,881 (GRCm39)	F129S	probably damaging	Het
Top3b	C	T	16: 16,708,526 (GRCm39)	R629*	probably null	Het
Trim17	T	A	11: 58,862,270 (GRCm39)	V434E	probably damaging	Het
Ttn	G	A	2: 76,615,327 (GRCm39)	P15051L	probably damaging	Het
Uggt2	A	T	14: 119,239,259 (GRCm39)	I1391N	probably damaging	Het
Usp8	A	T	2: 126,596,958 (GRCm39)	M923L	probably damaging	Het
Vmn1r176	T	C	7: 23,534,463 (GRCm39)	H230R	possibly damaging	Het
Vmn1r217	C	A	13: 23,298,159 (GRCm39)	D248Y	probably damaging	Het
Vmn2r14	A	T	5: 109,363,976 (GRCm39)	C647S	probably damaging	Het
Vwa5b1	A	G	4: 138,332,851 (GRCm39)	I237T	probably damaging	Het
Zan	T	A	5: 137,391,423 (GRCm39)	D4687V	unknown	Het
Zfp273	T	C	13: 67,973,484 (GRCm39)	V204A	probably benign	Het
Zfp956	T	G	6: 47,928,987 (GRCm39)		probably benign	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
R4944:Cdh2	UTSW	18	16,783,466 (GRCm39)	missense	probably damaging	0.99
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'- AAGGCACTGCTCTCTTTAACAC -3'
(R):5'- TGATGCTCCATGGCCTTTG -3'

Sequencing Primer
(F):5'- GCACTGCTCTCTTTAACACACAGG -3'
(R):5'- ATACCTCCCGGGATCACTG -3'

Posted On

2016-03-01