Mutagenetix > Incidental Mutation

Incidental Mutation 'R4724:Nedd9'

354718

Institutional Source

Beutler Lab

Gene Symbol

Nedd9

Ensembl Gene

ENSMUSG00000021365

Gene Name

neural precursor cell expressed, developmentally down-regulated gene 9

Synonyms

Cas-L, HEF1, CasL, E230025G09Rik

MMRRC Submission

041988-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4724 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

41463392-41640836 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 41470073 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 360 (V360A)

Ref Sequence

ENSEMBL: ENSMUSP00000021794 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021794] [ENSMUST00000163623] [ENSMUST00000224803]

AlphaFold

O35177

Predicted Effect

possibly damaging
Transcript: ENSMUST00000021794
AA Change: V360A

PolyPhen 2 Score 0.500 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000021794
Gene: ENSMUSG00000021365
AA Change: V360A

Domain	Start	End	E-Value	Type
SH3	6	64	3.78e-17	SMART
internal_repeat_1	151	218	1.33e-7	PROSPERO
low complexity region	368	396	N/A	INTRINSIC
Pfam:Serine_rich	403	561	3.2e-66	PFAM
Pfam:DUF3513	611	828	1.4e-91	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000163623
AA Change: V360A

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000125773
Gene: ENSMUSG00000021365
AA Change: V360A

Domain	Start	End	E-Value	Type
SH3	6	64	3.78e-17	SMART
internal_repeat_1	151	218	1.42e-7	PROSPERO
low complexity region	368	396	N/A	INTRINSIC
Pfam:Serine_rich	403	559	2.7e-60	PFAM
Pfam:DUF3513	618	827	1e-81	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000224803

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the CRK-associated substrates family. Members of this family are adhesion docking molecules that mediate protein-protein interactions for signal transduction pathways. This protein is a focal adhesion protein that acts as a scaffold to regulate signaling complexes important in cell attachment, migration and invasion as well as apoptosis and the cell cycle. This protein has also been reported to have a role in cancer metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
PHENOTYPE: Mice homozygous for one null allele exhibit impaired lymphocyte trafficking and a deficit of splenic marginal zone B cells. Mice homozygous for another null allele display impaired spatial learning and decreased hippocampal dendritic spine densities. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933434E20Rik	C	G	3: 89,960,848 (GRCm39)	Q34E	probably damaging	Het
4933434E20Rik	G	T	3: 89,960,890 (GRCm39)	V48F	probably damaging	Het
4933434E20Rik	A	T	3: 89,960,849 (GRCm39)	Q34L	probably damaging	Het
Abra	T	C	15: 41,729,302 (GRCm39)	D366G	probably damaging	Het
Acvr2a	T	C	2: 48,760,447 (GRCm39)	S68P	probably damaging	Het
Adam28	T	A	14: 68,864,326 (GRCm39)	R492S	probably damaging	Het
Adamts1	T	A	16: 85,599,393 (GRCm39)	E69V	probably benign	Het
Adgra1	A	T	7: 139,455,505 (GRCm39)	M378L	probably benign	Het
Adgra2	T	A	8: 27,588,850 (GRCm39)	N101K	possibly damaging	Het
Adhfe1	T	A	1: 9,646,475 (GRCm39)	F449L	probably damaging	Het
Akap6	T	A	12: 52,842,668 (GRCm39)	S5R	possibly damaging	Het
Akap9	G	A	5: 4,105,339 (GRCm39)	R2883Q	probably benign	Het
Ank3	T	A	10: 69,542,688 (GRCm39)	I16N	probably benign	Het
Api5	A	T	2: 94,253,816 (GRCm39)	F296I	possibly damaging	Het
Ceacam14	G	T	7: 17,547,975 (GRCm39)		probably null	Het
Cep295	C	T	9: 15,242,128 (GRCm39)	G1768S	probably damaging	Het
Cldn12	A	G	5: 5,558,385 (GRCm39)	F14S	probably damaging	Het
Cp	C	A	3: 20,026,811 (GRCm39)	T413K	probably benign	Het
Ctdsp2	T	G	10: 126,828,938 (GRCm39)	V104G	probably damaging	Het
Ctrc	T	A	4: 141,573,607 (GRCm39)		probably null	Het
Dbt	T	C	3: 116,326,945 (GRCm39)	I98T	probably damaging	Het
Dcaf10	G	A	4: 45,372,769 (GRCm39)	R394Q	possibly damaging	Het
Dctn1	T	A	6: 83,166,920 (GRCm39)	M257K	possibly damaging	Het
Depp1	T	A	6: 116,629,096 (GRCm39)	C146*	probably null	Het
Dlgap5	C	T	14: 47,638,977 (GRCm39)		probably null	Het
Drd3	G	T	16: 43,643,164 (GRCm39)	E467*	probably null	Het
Exoc8	A	G	8: 125,623,989 (GRCm39)	V126A	probably benign	Het
Fam185a	T	A	5: 21,660,785 (GRCm39)	S267T	probably damaging	Het
Fhod1	T	C	8: 106,064,493 (GRCm39)		probably benign	Het
Fn1	T	C	1: 71,687,307 (GRCm39)		probably null	Het
Gadl1	A	T	9: 115,783,685 (GRCm39)	T214S	possibly damaging	Het
Gem	G	T	4: 11,706,074 (GRCm39)	R54L	probably damaging	Het
Ghr	A	G	15: 3,355,422 (GRCm39)	V287A	probably benign	Het
Gm3642	G	A	14: 18,212,879 (GRCm39)	T215I	probably benign	Het
Grip1	T	A	10: 119,874,588 (GRCm39)	I732K	probably benign	Het
Gtpbp2	A	T	17: 46,478,147 (GRCm39)		probably null	Het
Heatr6	C	T	11: 83,670,374 (GRCm39)	R976*	probably null	Het
Hipk2	T	A	6: 38,675,327 (GRCm39)	T1084S	probably benign	Het
Hmcn1	T	C	1: 150,570,584 (GRCm39)		probably null	Het
Hspg2	T	A	4: 137,249,438 (GRCm39)	M1328K	probably damaging	Het
Ifna4	C	A	4: 88,760,519 (GRCm39)	T141K	probably benign	Het
Ighv1-64	A	G	12: 115,471,466 (GRCm39)	V17A	probably benign	Het
Iqgap2	G	T	13: 95,772,005 (GRCm39)	N1391K	possibly damaging	Het
Irf7	A	T	7: 140,844,648 (GRCm39)	L148Q	possibly damaging	Het
Kat6b	G	A	14: 21,711,030 (GRCm39)	R768K	probably benign	Het
Lepr	G	A	4: 101,622,562 (GRCm39)	W447*	probably null	Het
Letmd1	A	G	15: 100,367,619 (GRCm39)	Y59C	probably damaging	Het
Lingo4	A	T	3: 94,310,183 (GRCm39)	K374*	probably null	Het
Loxl4	G	T	19: 42,596,785 (GRCm39)	D62E	probably benign	Het
Lrfn2	A	G	17: 49,377,462 (GRCm39)	D181G	probably damaging	Het
Lrrc71	A	T	3: 87,646,481 (GRCm39)	F526L	probably damaging	Het
Ltbp1	A	T	17: 75,620,003 (GRCm39)	M711L	probably damaging	Het
Mcm7	A	T	5: 138,167,387 (GRCm39)	D78E	probably damaging	Het
Mdh1	T	C	11: 21,512,957 (GRCm39)	N136D	probably damaging	Het
Meltf	T	A	16: 31,711,323 (GRCm39)	N515K	probably benign	Het
Mis18bp1	T	A	12: 65,205,513 (GRCm39)	T220S	probably benign	Het
Mtss1	C	T	15: 58,953,367 (GRCm39)	V4M	probably damaging	Het
Nacc2	A	T	2: 25,980,185 (GRCm39)	F84I	probably damaging	Het
Nek11	T	A	9: 105,270,169 (GRCm39)	I18F	possibly damaging	Het
Nkd2	C	T	13: 73,995,124 (GRCm39)	V13M	probably damaging	Het
Nkx6-3	A	G	8: 23,646,285 (GRCm39)	I152V	probably damaging	Het
Npdc1	G	A	2: 25,298,957 (GRCm39)	D284N	probably damaging	Het
Oprm1	A	T	10: 6,708,656 (GRCm39)	R16*	probably null	Het
Or1e16	A	T	11: 73,285,981 (GRCm39)	I289N	probably damaging	Het
Or51b4	A	G	7: 103,530,856 (GRCm39)	V198A	probably benign	Het
Or5an1	T	C	19: 12,260,460 (GRCm39)	L16P	probably damaging	Het
Or5p69	T	A	7: 107,967,205 (GRCm39)	F169L	probably benign	Het
Or6d15	T	C	6: 116,559,898 (GRCm39)	N3S	probably damaging	Het
Or7a36	A	G	10: 78,820,356 (GRCm39)	H244R	probably damaging	Het
Ostf1	G	A	19: 18,571,231 (GRCm39)	P62L	probably damaging	Het
Pcdha2	A	T	18: 37,073,568 (GRCm39)	T400S	possibly damaging	Het
Pcdha5	A	T	18: 37,094,549 (GRCm39)	T353S	possibly damaging	Het
Pelo	A	G	13: 115,225,271 (GRCm39)	F318S	probably damaging	Het
Polr2f	T	C	15: 79,030,269 (GRCm39)	V36A	probably benign	Het
Ppan	G	A	9: 20,799,806 (GRCm39)	R41H	probably benign	Het
Ppp1r21	C	T	17: 88,863,019 (GRCm39)	R253*	probably null	Het
Prf1	T	A	10: 61,139,487 (GRCm39)	W482R	probably damaging	Het
Ralgapa2	T	C	2: 146,187,453 (GRCm39)	T1397A	possibly damaging	Het
Rev3l	T	A	10: 39,722,802 (GRCm39)	Y2598*	probably null	Het
Scaf11	G	T	15: 96,312,729 (GRCm39)	D1437E	probably benign	Het
Sec23a	C	T	12: 59,025,292 (GRCm39)	G510R	probably damaging	Het
Sel1l2	A	G	2: 140,082,847 (GRCm39)	M597T	probably damaging	Het
Slc11a2	A	T	15: 100,304,219 (GRCm39)	S160T	possibly damaging	Het
Slc18a1	A	T	8: 69,526,301 (GRCm39)	L129*	probably null	Het
Smg8	A	C	11: 86,977,047 (GRCm39)	L178R	probably benign	Het
Sp4	T	C	12: 118,225,544 (GRCm39)	T607A	probably benign	Het
Ssbp2	A	G	13: 91,836,933 (GRCm39)	D266G	possibly damaging	Het
Sstr3	A	T	15: 78,423,897 (GRCm39)	Y283*	probably null	Het
Stk32b	C	T	5: 37,612,278 (GRCm39)		probably null	Het
Svep1	T	C	4: 58,070,752 (GRCm39)	T2345A	possibly damaging	Het
Synpo2	A	G	3: 122,907,940 (GRCm39)	S459P	probably damaging	Het
Sytl2	A	G	7: 89,998,000 (GRCm39)	M1V	probably null	Het
Tas2r102	T	A	6: 132,739,520 (GRCm39)	W143R	probably damaging	Het
Thy1	T	C	9: 43,958,645 (GRCm39)	V129A	probably damaging	Het
Tlr2	A	T	3: 83,745,492 (GRCm39)	I197N	probably damaging	Het
Tmem101	A	G	11: 102,044,269 (GRCm39)	I206T	probably benign	Het
Tmem108	A	G	9: 103,376,688 (GRCm39)	S254P	possibly damaging	Het
Tmem198b	T	C	10: 128,637,350 (GRCm39)	Q263R	probably damaging	Het
Vangl1	T	C	3: 102,091,870 (GRCm39)	D72G	probably damaging	Het
Vmn1r4	T	A	6: 56,934,349 (GRCm39)	D284E	probably benign	Het
Vmn2r31	G	A	7: 7,387,757 (GRCm39)	L605F	possibly damaging	Het
Zfand4	T	C	6: 116,250,780 (GRCm39)	V70A	probably damaging	Het
Zfp54	A	G	17: 21,653,665 (GRCm39)	E53G	probably damaging	Het
Zfp541	A	T	7: 15,815,612 (GRCm39)	I805F	probably damaging	Het
Zfp976	T	C	7: 42,262,457 (GRCm39)	H460R	possibly damaging	Het

Other mutations in Nedd9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01109:Nedd9	APN	13	41,469,710 (GRCm39)	missense	probably benign	0.00
IGL01412:Nedd9	APN	13	41,469,262 (GRCm39)	nonsense	probably null
IGL01669:Nedd9	APN	13	41,492,111 (GRCm39)	missense	probably damaging	0.99
IGL02543:Nedd9	APN	13	41,470,211 (GRCm39)	missense	probably damaging	1.00
IGL03302:Nedd9	APN	13	41,492,330 (GRCm39)	missense	probably damaging	0.99
hebei	UTSW	13	41,492,455 (GRCm39)	nonsense	probably null
sheep	UTSW	13	41,471,438 (GRCm39)	missense	probably benign	0.33
yanzhao	UTSW	13	41,465,270 (GRCm39)	missense	probably damaging	1.00
R1157:Nedd9	UTSW	13	41,467,979 (GRCm39)	splice site	probably null
R1611:Nedd9	UTSW	13	41,470,406 (GRCm39)	missense	probably benign
R1669:Nedd9	UTSW	13	41,465,270 (GRCm39)	missense	probably damaging	1.00
R1718:Nedd9	UTSW	13	41,492,402 (GRCm39)	missense	probably damaging	1.00
R1775:Nedd9	UTSW	13	41,471,438 (GRCm39)	missense	probably benign	0.33
R1971:Nedd9	UTSW	13	41,492,424 (GRCm39)	missense	probably damaging	1.00
R2107:Nedd9	UTSW	13	41,492,455 (GRCm39)	nonsense	probably null
R2341:Nedd9	UTSW	13	41,469,987 (GRCm39)	missense	probably damaging	1.00
R4362:Nedd9	UTSW	13	41,471,429 (GRCm39)	missense	probably damaging	0.99
R4363:Nedd9	UTSW	13	41,471,429 (GRCm39)	missense	probably damaging	0.99
R4707:Nedd9	UTSW	13	41,492,051 (GRCm39)	critical splice donor site	probably null
R4795:Nedd9	UTSW	13	41,471,376 (GRCm39)	missense	probably benign	0.12
R4796:Nedd9	UTSW	13	41,471,376 (GRCm39)	missense	probably benign	0.12
R4853:Nedd9	UTSW	13	41,469,837 (GRCm39)	missense	probably benign	0.01
R4934:Nedd9	UTSW	13	41,492,411 (GRCm39)	missense	probably damaging	1.00
R5020:Nedd9	UTSW	13	41,469,270 (GRCm39)	missense	probably damaging	1.00
R5070:Nedd9	UTSW	13	41,470,074 (GRCm39)	missense	probably benign	0.00
R5585:Nedd9	UTSW	13	41,469,950 (GRCm39)	missense	probably damaging	1.00
R5588:Nedd9	UTSW	13	41,469,437 (GRCm39)	missense	possibly damaging	0.76
R6310:Nedd9	UTSW	13	41,471,928 (GRCm39)	missense	probably benign	0.00
R6634:Nedd9	UTSW	13	41,465,584 (GRCm39)	missense	probably damaging	1.00
R6729:Nedd9	UTSW	13	41,469,278 (GRCm39)	missense	probably damaging	0.99
R7114:Nedd9	UTSW	13	41,492,099 (GRCm39)	missense	probably benign
R7172:Nedd9	UTSW	13	41,470,280 (GRCm39)	missense	probably benign	0.01
R7477:Nedd9	UTSW	13	41,471,956 (GRCm39)	missense	probably benign	0.02
R7665:Nedd9	UTSW	13	41,469,785 (GRCm39)	missense	probably benign	0.01
R7672:Nedd9	UTSW	13	41,492,198 (GRCm39)	missense	possibly damaging	0.69
R7810:Nedd9	UTSW	13	41,465,483 (GRCm39)	missense	possibly damaging	0.52
R7893:Nedd9	UTSW	13	41,469,265 (GRCm39)	missense	probably damaging	1.00
R7952:Nedd9	UTSW	13	41,470,431 (GRCm39)	missense	probably damaging	1.00
R8215:Nedd9	UTSW	13	41,492,319 (GRCm39)	missense	probably benign	0.14
R8399:Nedd9	UTSW	13	41,471,950 (GRCm39)	nonsense	probably null
R8959:Nedd9	UTSW	13	41,469,758 (GRCm39)	missense	probably damaging	0.98
R9039:Nedd9	UTSW	13	41,471,984 (GRCm39)	missense	probably damaging	1.00
R9236:Nedd9	UTSW	13	41,492,153 (GRCm39)	missense	possibly damaging	0.86
R9663:Nedd9	UTSW	13	41,469,941 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGTGACATGAGGCTGCACAC -3'
(R):5'- ACACCAGAGCTTTTCCCTGC -3'

Sequencing Primer
(F):5'- ACACCCATCTCCAGGGTCTG -3'
(R):5'- AGAGCTTTTCCCTGCACCATG -3'

Posted On

2015-10-21