Mutagenetix > Incidental Mutation

Incidental Mutation 'R4576:Cdh9'

342500

Institutional Source

Beutler Lab

Gene Symbol

Cdh9

Ensembl Gene

ENSMUSG00000025370

Gene Name

cadherin 9

Synonyms

T1-cadherin

MMRRC Submission

041799-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.105) question?

Stock #

R4576 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

16728842-16857180 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 16832325 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 404 (V404A)

Ref Sequence

ENSEMBL: ENSMUSP00000154022 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026432] [ENSMUST00000228307]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000026432
AA Change: V404A

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000026432
Gene: ENSMUSG00000025370
AA Change: V404A

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
CA	75	156	2.84e-15	SMART
CA	180	265	5.63e-28	SMART
CA	289	381	1.12e-13	SMART
CA	404	485	8.03e-24	SMART
CA	508	595	1.34e-2	SMART
transmembrane domain	613	635	N/A	INTRINSIC
Pfam:Cadherin_C	638	782	1.5e-54	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227900

Predicted Effect

possibly damaging
Transcript: ENSMUST00000228307
AA Change: V404A

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)

Meta Mutation Damage Score

0.3256

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

98% (84/86)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous knockout results in the formation of abnormal axonal arbors in some retinal type 5 bipolar cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adhfe1	A	T	1: 9,623,979 (GRCm39)	D160V	probably damaging	Het
Ano9	T	C	7: 140,684,051 (GRCm39)	Q538R	probably damaging	Het
Atp4a	A	G	7: 30,417,147 (GRCm39)	D510G	probably benign	Het
Atp8a1	T	C	5: 67,973,158 (GRCm39)		probably benign	Het
Auts2	C	T	5: 132,287,773 (GRCm39)	G70E	probably benign	Het
C7	A	G	15: 5,032,238 (GRCm39)	S658P	probably damaging	Het
Cfap54	C	T	10: 92,879,090 (GRCm39)		probably null	Het
Chml	G	T	1: 175,514,506 (GRCm39)	Q129K	probably damaging	Het
Chst2	T	C	9: 95,287,224 (GRCm39)	H374R	probably damaging	Het
Cimip2a	T	C	2: 25,110,300 (GRCm39)	S71P	probably benign	Het
Cirbp	A	G	10: 80,006,075 (GRCm39)	K84E	probably damaging	Het
Cln6	G	T	9: 62,746,231 (GRCm39)	Q23H	probably benign	Het
Cntn5	A	G	9: 9,673,297 (GRCm39)	M801T	probably benign	Het
Dapk1	A	T	13: 60,869,636 (GRCm39)	M293L	probably benign	Het
Ddx11	A	G	17: 66,457,721 (GRCm39)	K869E	probably damaging	Het
Ddx17	A	T	15: 79,425,347 (GRCm39)	M108K	probably benign	Het
Dnaaf5	C	A	5: 139,171,394 (GRCm39)	A557D	probably damaging	Het
Ecpas	A	T	4: 58,834,708 (GRCm39)		probably benign	Het
Edil3	T	C	13: 89,467,850 (GRCm39)	Y452H	probably damaging	Het
Elfn1	T	C	5: 139,957,808 (GRCm39)	S271P	probably benign	Het
Enah	G	A	1: 181,747,128 (GRCm39)	S298L	possibly damaging	Het
Exoc7	T	C	11: 116,180,009 (GRCm39)	*685W	probably null	Het
Fgfbp1	C	T	5: 44,136,806 (GRCm39)	R162H	probably benign	Het
Foxj3	A	G	4: 119,478,860 (GRCm39)	S439G	unknown	Het
Fzd9	A	G	5: 135,279,166 (GRCm39)	S240P	probably damaging	Het
Gin1	A	G	1: 97,720,064 (GRCm39)	D442G	probably damaging	Het
Gm10804	C	T	2: 93,299,014 (GRCm39)		noncoding transcript	Het
Grhl3	G	T	4: 135,288,562 (GRCm39)	T41K	probably damaging	Het
H6pd	A	T	4: 150,078,933 (GRCm39)	D243E	probably damaging	Het
Heatr6	T	A	11: 83,655,826 (GRCm39)	S306T	probably benign	Het
Hkdc1	T	C	10: 62,221,622 (GRCm39)	D812G	possibly damaging	Het
Hmcn1	G	T	1: 150,610,238 (GRCm39)	T1477K	probably benign	Het
Ift80	A	G	3: 68,857,863 (GRCm39)	S261P	possibly damaging	Het
Kcnu1	A	T	8: 26,380,048 (GRCm39)	D424V	probably benign	Het
Kctd1	A	G	18: 15,140,757 (GRCm39)	S658P	probably damaging	Het
Klk12	A	G	7: 43,422,667 (GRCm39)	D198G	probably damaging	Het
Kntc1	T	G	5: 123,904,018 (GRCm39)	L345R	probably damaging	Het
Llph-ps2	A	G	X: 13,084,690 (GRCm39)		noncoding transcript	Het
Lpxn	T	C	19: 12,810,654 (GRCm39)	I366T	probably benign	Het
Lrp1	ACAGGCGC	AC	10: 127,376,057 (GRCm39)		probably benign	Het
Maml3	G	A	3: 51,763,927 (GRCm39)	Q346*	probably null	Het
Mef2a	T	C	7: 66,890,187 (GRCm39)	N131S	probably benign	Het
Mlc1	G	A	15: 88,858,740 (GRCm39)	T136M	probably damaging	Het
Mplkipl1	C	T	19: 61,164,364 (GRCm39)	G24R	unknown	Het
Pcdhga9	A	C	18: 37,870,881 (GRCm39)	N237H	probably damaging	Het
Pde4dip	C	A	3: 97,661,565 (GRCm39)	E657D	probably damaging	Het
Pknox2	A	G	9: 36,834,844 (GRCm39)		probably benign	Het
Plcb3	C	T	19: 6,936,415 (GRCm39)		probably benign	Het
Plxnd1	G	A	6: 115,945,005 (GRCm39)	A99V	probably benign	Het
Pnpla2	T	C	7: 141,037,257 (GRCm39)	S87P	probably damaging	Het
Ppp1r14c	G	T	10: 3,316,912 (GRCm39)	K82N	probably damaging	Het
Pum3	G	A	19: 27,393,308 (GRCm39)	T389M	probably benign	Het
Pxdn	A	T	12: 30,061,922 (GRCm39)	T1165S	probably benign	Het
Rasgrf2	T	C	13: 92,044,529 (GRCm39)	D925G	possibly damaging	Het
Samhd1	A	T	2: 156,943,670 (GRCm39)	C615S	probably damaging	Het
Sec16a	A	T	2: 26,321,131 (GRCm39)	Y1320*	probably null	Het
Slco6b1	T	A	1: 96,916,422 (GRCm39)		noncoding transcript	Het
Slitrk6	C	A	14: 110,987,602 (GRCm39)	V702F	probably benign	Het
Spata31d1b	C	A	13: 59,864,675 (GRCm39)	H608N	probably damaging	Het
Spef1l	A	G	7: 139,558,043 (GRCm39)	I51T	probably damaging	Het
Srpra	T	C	9: 35,125,904 (GRCm39)	I394T	possibly damaging	Het
Svop	C	T	5: 114,203,743 (GRCm39)	V13M	probably damaging	Het
Tacc3	T	A	5: 33,818,841 (GRCm39)		probably benign	Het
Tango2	A	T	16: 18,119,392 (GRCm39)	D146E	probably damaging	Het
Thbs1	G	A	2: 117,949,897 (GRCm39)	R624Q	probably damaging	Het
Tmem161a	T	C	8: 70,634,713 (GRCm39)		probably null	Het
Tmem175	A	G	5: 108,792,468 (GRCm39)	D248G	possibly damaging	Het
Traf3ip2	A	G	10: 39,510,650 (GRCm39)	N308D	probably damaging	Het
Trim30b	T	C	7: 104,006,538 (GRCm39)	Y106C	possibly damaging	Het
Trip11	G	A	12: 101,852,499 (GRCm39)	Q521*	probably null	Het
Tssk5	C	T	15: 76,256,668 (GRCm39)	R280Q	probably benign	Het
Ttc16	A	T	2: 32,660,071 (GRCm39)	F246I	probably benign	Het
Unc79	T	C	12: 102,968,062 (GRCm39)		probably benign	Het
Vmn1r74	A	G	7: 11,580,696 (GRCm39)		probably null	Het
Vmn2r16	A	T	5: 109,511,665 (GRCm39)	Y624F	possibly damaging	Het
Zc3h4	G	A	7: 16,168,579 (GRCm39)	R896H	unknown	Het
Zfp941	T	A	7: 140,391,503 (GRCm39)	K619*	probably null	Het
Zfp970	A	T	2: 177,167,473 (GRCm39)	H349L	probably damaging	Het

Other mutations in Cdh9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00429:Cdh9	APN	15	16,828,448 (GRCm39)	missense	probably damaging	1.00
IGL00555:Cdh9	APN	15	16,823,492 (GRCm39)	missense	probably damaging	1.00
IGL01110:Cdh9	APN	15	16,856,012 (GRCm39)	missense	possibly damaging	0.63
IGL01432:Cdh9	APN	15	16,831,033 (GRCm39)	missense	probably damaging	1.00
IGL01768:Cdh9	APN	15	16,778,311 (GRCm39)	missense	possibly damaging	0.51
IGL02043:Cdh9	APN	15	16,856,318 (GRCm39)	missense	probably damaging	1.00
IGL02304:Cdh9	APN	15	16,848,687 (GRCm39)	missense	probably benign	0.01
IGL02380:Cdh9	APN	15	16,856,086 (GRCm39)	missense	possibly damaging	0.79
IGL02505:Cdh9	APN	15	16,856,075 (GRCm39)	missense	probably damaging	1.00
IGL02675:Cdh9	APN	15	16,849,162 (GRCm39)	splice site	probably null
IGL02679:Cdh9	APN	15	16,832,316 (GRCm39)	missense	probably damaging	0.97
IGL03288:Cdh9	APN	15	16,856,135 (GRCm39)	missense	probably damaging	1.00
R0426:Cdh9	UTSW	15	16,823,540 (GRCm39)	critical splice donor site	probably null
R0726:Cdh9	UTSW	15	16,831,130 (GRCm39)	missense	probably benign	0.00
R1335:Cdh9	UTSW	15	16,850,878 (GRCm39)	missense	probably benign	0.00
R1368:Cdh9	UTSW	15	16,848,568 (GRCm39)	splice site	probably benign
R1766:Cdh9	UTSW	15	16,778,392 (GRCm39)	missense	probably damaging	1.00
R1916:Cdh9	UTSW	15	16,823,361 (GRCm39)	missense	probably benign	0.03
R2325:Cdh9	UTSW	15	16,778,286 (GRCm39)	missense	probably benign
R2424:Cdh9	UTSW	15	16,850,440 (GRCm39)	missense	probably damaging	1.00
R3104:Cdh9	UTSW	15	16,855,900 (GRCm39)	missense	probably damaging	1.00
R3837:Cdh9	UTSW	15	16,823,524 (GRCm39)	nonsense	probably null
R3839:Cdh9	UTSW	15	16,823,524 (GRCm39)	nonsense	probably null
R4241:Cdh9	UTSW	15	16,849,165 (GRCm39)	critical splice acceptor site	probably null
R4248:Cdh9	UTSW	15	16,850,474 (GRCm39)	missense	probably benign	0.00
R4679:Cdh9	UTSW	15	16,851,045 (GRCm39)	missense	probably benign
R4896:Cdh9	UTSW	15	16,778,242 (GRCm39)	missense	probably benign	0.12
R4961:Cdh9	UTSW	15	16,850,914 (GRCm39)	missense	probably benign
R5050:Cdh9	UTSW	15	16,778,233 (GRCm39)	missense	probably benign	0.12
R5089:Cdh9	UTSW	15	16,778,362 (GRCm39)	missense	probably damaging	1.00
R5268:Cdh9	UTSW	15	16,851,099 (GRCm39)	missense	probably benign
R5567:Cdh9	UTSW	15	16,855,930 (GRCm39)	missense	probably damaging	1.00
R5646:Cdh9	UTSW	15	16,823,371 (GRCm39)	missense	probably damaging	1.00
R5894:Cdh9	UTSW	15	16,832,186 (GRCm39)	missense	possibly damaging	0.47
R6440:Cdh9	UTSW	15	16,823,509 (GRCm39)	missense	probably benign	0.01
R6441:Cdh9	UTSW	15	16,823,509 (GRCm39)	missense	probably benign	0.01
R7225:Cdh9	UTSW	15	16,856,159 (GRCm39)	missense	probably damaging	1.00
R7247:Cdh9	UTSW	15	16,778,341 (GRCm39)	missense	probably damaging	1.00
R7593:Cdh9	UTSW	15	16,823,261 (GRCm39)	missense	probably damaging	1.00
R7615:Cdh9	UTSW	15	16,856,316 (GRCm39)	missense	probably damaging	1.00
R7632:Cdh9	UTSW	15	16,851,115 (GRCm39)	splice site	probably null
R7991:Cdh9	UTSW	15	16,828,489 (GRCm39)	missense	probably damaging	1.00
R8035:Cdh9	UTSW	15	16,831,152 (GRCm39)	missense	probably damaging	0.97
R8834:Cdh9	UTSW	15	16,850,964 (GRCm39)	missense	probably damaging	1.00
R8909:Cdh9	UTSW	15	16,848,610 (GRCm39)	missense	probably damaging	1.00
R8936:Cdh9	UTSW	15	16,831,162 (GRCm39)	critical splice donor site	probably null
R8973:Cdh9	UTSW	15	16,831,131 (GRCm39)	missense	possibly damaging	0.78
R9138:Cdh9	UTSW	15	16,823,273 (GRCm39)	missense	probably damaging	1.00
R9305:Cdh9	UTSW	15	16,832,138 (GRCm39)	missense	probably damaging	1.00
RF006:Cdh9	UTSW	15	16,855,916 (GRCm39)	missense	probably damaging	0.97
X0062:Cdh9	UTSW	15	16,848,625 (GRCm39)	missense	possibly damaging	0.81
Z1177:Cdh9	UTSW	15	16,850,450 (GRCm39)	missense	probably benign	0.16

Predicted Primers

PCR Primer
(F):5'- TGCAAGTAATACCCACCCTG -3'
(R):5'- GGTTCTCAGACTCACACAGTG -3'

Sequencing Primer
(F):5'- GTAATACCCACCCTGATCCTCG -3'
(R):5'- CTCACACAGTGTCTAATTTTTGGAGC -3'

Posted On

2015-09-24