Mutagenetix > Incidental Mutation

Incidental Mutation 'R9663:Nedd9'

727707

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9663 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

41463392-41640836 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 41469941 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 404 (D404G)

Ref Sequence

ENSEMBL: ENSMUSP00000021794 (fasta)

Gene Model

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

AlphaFold

O35177

Predicted Effect

probably damaging
Transcript: ENSMUST00000021794
AA Change: D404G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021794
Gene: ENSMUSG00000021365
AA Change: D404G

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

probably damaging
Transcript: ENSMUST00000163623
AA Change: D404G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000125773
Gene: ENSMUSG00000021365
AA Change: D404G

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alkbh6	T	C	7: 30,013,371 (GRCm39)	S161P	probably damaging	Het
Alppl2	T	A	1: 87,015,753 (GRCm39)	H297L	probably benign	Het
Angptl2	A	G	2: 33,118,231 (GRCm39)	R2G	probably benign	Het
Arhgef15	T	A	11: 68,845,255 (GRCm39)	N199I	probably damaging	Het
Asns	A	T	6: 7,680,132 (GRCm39)	I328K	probably damaging	Het
Atad2	G	T	15: 57,971,540 (GRCm39)	T734K	probably benign	Het
Capn3	A	C	2: 120,316,859 (GRCm39)	M283L	probably benign	Het
Catsperd	T	A	17: 56,960,751 (GRCm39)	C384S	possibly damaging	Het
Cd101	A	G	3: 100,911,222 (GRCm39)	V816A	probably benign	Het
Cd5	T	G	19: 10,703,858 (GRCm39)	D68A	probably benign	Het
Ceacam18	G	A	7: 43,288,764 (GRCm39)	V172M	probably damaging	Het
Cfap100	G	A	6: 90,386,328 (GRCm39)	R276C		Het
Clip2	C	T	5: 134,533,616 (GRCm39)	R487Q	probably benign	Het
Creb3l2	A	G	6: 37,356,926 (GRCm39)	V47A	probably damaging	Het
Crebbp	T	A	16: 3,933,654 (GRCm39)	E1017D	probably damaging	Het
Cttn	T	C	7: 144,011,461 (GRCm39)	D116G	probably damaging	Het
Cyp2c65	A	G	19: 39,079,070 (GRCm39)		probably null	Het
Dcaf13	C	T	15: 38,982,178 (GRCm39)	T48I	possibly damaging	Het
Dsc2	T	A	18: 20,171,205 (GRCm39)	D598V	probably damaging	Het
Dtx3	G	A	10: 127,028,518 (GRCm39)	T237I	probably damaging	Het
E130308A19Rik	A	G	4: 59,719,764 (GRCm39)	E432G	possibly damaging	Het
Eps15	G	A	4: 109,179,270 (GRCm39)	V219I	probably benign	Het
Ext1	A	G	15: 53,208,456 (GRCm39)	S102P	probably damaging	Het
Fam151a	A	T	4: 106,604,894 (GRCm39)	I419L	possibly damaging	Het
Fam89a	C	T	8: 125,478,436 (GRCm39)	G38D	probably damaging	Het
Fdx2	G	T	9: 20,984,717 (GRCm39)	A29E	probably benign	Het
Hhla1	G	A	15: 65,813,630 (GRCm39)	T234I	probably damaging	Het
Hspb6	G	A	7: 30,253,714 (GRCm39)	V76M	probably damaging	Het
Ighmbp2	C	A	19: 3,315,325 (GRCm39)	K698N	probably benign	Het
Invs	A	G	4: 48,426,218 (GRCm39)	I1002V	probably damaging	Het
Itga8	A	C	2: 12,196,580 (GRCm39)	F612L	probably benign	Het
Kcnma1	G	T	14: 24,053,897 (GRCm39)	F99L	probably benign	Het
Klf11	A	G	12: 24,705,731 (GRCm39)	Y395C	probably damaging	Het
Kplce	A	T	3: 92,776,283 (GRCm39)	N133K	probably benign	Het
Lama4	G	A	10: 38,923,944 (GRCm39)	E451K	probably damaging	Het
Lrr1	A	G	12: 69,221,884 (GRCm39)	Y342C	probably damaging	Het
Lrrc18	A	T	14: 32,731,021 (GRCm39)	M187L	probably benign	Het
Luc7l3	A	G	11: 94,187,756 (GRCm39)	S311P	unknown	Het
Lypd3	T	A	7: 24,338,349 (GRCm39)	S133R	probably damaging	Het
Mcm5	C	T	8: 75,844,168 (GRCm39)	S313F	probably benign	Het
Mug1	T	A	6: 121,859,699 (GRCm39)	S1233T	probably benign	Het
Mug1	A	T	6: 121,857,463 (GRCm39)	E1062D	probably benign	Het
Myh7	T	C	14: 55,221,098 (GRCm39)	K942E	probably damaging	Het
Nisch	C	A	14: 30,895,625 (GRCm39)	A1022S	probably damaging	Het
Nkx3-1	A	G	14: 69,429,321 (GRCm39)	D113G	probably benign	Het
Or1ad6	T	C	11: 50,860,165 (GRCm39)	F107L	probably benign	Het
Or6c1b	A	T	10: 129,272,929 (GRCm39)	I83F	probably damaging	Het
Or6c215	A	G	10: 129,637,497 (GRCm39)	F299S	probably benign	Het
Otub1	C	T	19: 7,176,813 (GRCm39)	G181D	probably damaging	Het
Palb2	T	C	7: 121,726,304 (GRCm39)	H522R	probably benign	Het
Pfpl	A	T	19: 12,407,459 (GRCm39)	D570V	probably damaging	Het
Phyhd1	A	G	2: 30,171,070 (GRCm39)	N271S	probably damaging	Het
Ptprm	T	C	17: 67,498,291 (GRCm39)	Q50R	probably benign	Het
Rfx2	C	A	17: 57,087,895 (GRCm39)	V499L	possibly damaging	Het
Sema5a	C	T	15: 32,673,546 (GRCm39)	Q795*	probably null	Het
Sf3a2	A	G	10: 80,637,309 (GRCm39)	N49S	probably damaging	Het
Sft2d1	T	G	17: 8,545,812 (GRCm39)	S156A	probably benign	Het
Slc14a1	C	A	18: 78,152,807 (GRCm39)	A367S	probably damaging	Het
Slc25a33	T	A	4: 149,836,913 (GRCm39)	T144S	probably benign	Het
Slc7a13	A	T	4: 19,818,818 (GRCm39)	K6M	possibly damaging	Het
Spata31e5	G	T	1: 28,816,536 (GRCm39)	H499N	probably benign	Het
Tfap2c	G	A	2: 172,399,213 (GRCm39)	D487N	probably damaging	Het
Thbs1	G	A	2: 117,949,897 (GRCm39)	R624Q	probably damaging	Het
Thsd4	A	G	9: 59,890,026 (GRCm39)	F857S	probably damaging	Het
Tnfrsf4	A	G	4: 156,100,884 (GRCm39)	I272V	probably benign	Het
Trak1	C	T	9: 121,220,924 (GRCm39)	R45C	probably benign	Het
Trpm2	A	G	10: 77,756,320 (GRCm39)	S1167P	probably benign	Het
Ttc14	A	T	3: 33,855,537 (GRCm39)	T161S	probably benign	Het
Ttll1	A	G	15: 83,380,579 (GRCm39)	V262A	possibly damaging	Het
Ttn	C	T	2: 76,715,357 (GRCm39)	E7912K	unknown	Het
Ufsp1	C	A	5: 137,293,545 (GRCm39)	P165Q	possibly damaging	Het
Usp19	T	G	9: 108,371,894 (GRCm39)	L390R	probably damaging	Het
Vegfc	G	T	8: 54,634,338 (GRCm39)	C339F	probably damaging	Het
Vmn2r6	A	T	3: 64,463,549 (GRCm39)	N428K	possibly damaging	Het
Wdr11	T	G	7: 129,210,647 (GRCm39)	V517G	probably damaging	Het
Xkr4	T	A	1: 3,286,519 (GRCm39)	D557V	probably benign	Het
Zan	C	A	5: 137,379,119 (GRCm39)	C5327F	unknown	Het
Zfp770	A	T	2: 114,026,949 (GRCm39)	N373K	probably benign	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
R4724:Nedd9	UTSW	13	41,470,073 (GRCm39)	missense	possibly damaging	0.50
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

Predicted Primers

PCR Primer
(F):5'- AGGCATTGGCTAAAGCTCCC -3'
(R):5'- AGAGACGGTGTCTACGATGTC -3'

Sequencing Primer
(F):5'- CCCTTGGCAAAATGGAGGTATTCTC -3'
(R):5'- TACGATGTCCCTCTGCACAAC -3'

Posted On

2022-10-06