Mutagenetix > Incidental Mutation

Incidental Mutation 'R2015:Nde1'

222907

Institutional Source

Beutler Lab

Gene Symbol

Nde1

Ensembl Gene

ENSMUSG00000022678

Gene Name

nudE neurodevelopment protein 1

Synonyms

mNudE, 2810027M15Rik

MMRRC Submission

040024-MU

Accession Numbers

Genbank: NM_023317; MGI: 1914453

Essential gene?

Probably essential (E-score: 0.861) question?

Stock #

R2015 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

14163275-14192928 bp(+) (GRCm38)

Type of Mutation

start gained

DNA Base Change (assembly)

A to T at 14169457 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000118005 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023359] [ENSMUST00000115795] [ENSMUST00000117958] [ENSMUST00000132316]

AlphaFold

Q9CZA6

Predicted Effect

probably benign
Transcript: ENSMUST00000023359

SMART Domains

Protein: ENSMUSP00000023359
Gene: ENSMUSG00000022678

Domain	Start	End	E-Value	Type
low complexity region	47	56	N/A	INTRINSIC
Pfam:NUDE_C	134	312	1.7e-50	PFAM
low complexity region	324	336	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115795

SMART Domains

Protein: ENSMUSP00000111461
Gene: ENSMUSG00000022678

Domain	Start	End	E-Value	Type
low complexity region	47	56	N/A	INTRINSIC
Pfam:NUDE_C	134	317	1.2e-40	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117958

SMART Domains

Protein: ENSMUSP00000112817
Gene: ENSMUSG00000022678

Domain	Start	End	E-Value	Type
low complexity region	47	56	N/A	INTRINSIC
Pfam:NUDE_C	134	317	9.8e-41	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127801

Predicted Effect

probably benign
Transcript: ENSMUST00000132316

SMART Domains

Protein: ENSMUSP00000118005
Gene: ENSMUSG00000022678

Domain	Start	End	E-Value	Type
PDB:2V71\|B	8	79	2e-14	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133249

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe mental retardation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
PHENOTYPE: Homozygous null mutants have a small brain with fewer neurons in the cerebral cortex and very thin superficial cortical layers. [provided by MGI curators]

Allele List at MGI

All alleles(37) : Targeted, knock-out(1) Gene trapped(36)

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006E09Rik	C	A	11: 101,987,218	H35Q	probably damaging	Het
1700015F17Rik	T	A	5: 5,455,964	I106L	probably benign	Het
Abca9	A	T	11: 110,131,846	M1022K	probably benign	Het
Abhd4	T	A	14: 54,262,832	H74Q	probably damaging	Het
Actg1	A	G	11: 120,346,810	S49P	possibly damaging	Het
Adcy8	C	T	15: 64,767,878	G678S	probably benign	Het
Aire	T	C	10: 78,042,958	D85G	probably damaging	Het
Akr1c18	T	A	13: 4,145,309	D50V	probably damaging	Het
Ankrd13a	C	A	5: 114,792,109	A185E	probably damaging	Het
Apc	A	G	18: 34,315,591	I1813V	probably damaging	Het
Armc8	A	T	9: 99,483,105	C661*	probably null	Het
Bbs10	C	T	10: 111,300,855	Q610*	probably null	Het
Blm	T	C	7: 80,502,399	E600G	probably damaging	Het
Bpifb9a	T	C	2: 154,268,200		probably null	Het
Cdk14	T	C	5: 5,380,082	K15R	probably benign	Het
Cdr1	A	G	X: 61,184,814	F249L	probably benign	Het
Cep250	A	C	2: 155,981,453	H1009P	probably damaging	Het
Clasp2	A	G	9: 113,911,500	T495A	possibly damaging	Het
Col19a1	C	G	1: 24,559,753	G53A	unknown	Het
Cpne1	G	A	2: 156,078,388	R166C	probably damaging	Het
Dtx3l	G	A	16: 35,936,427	H129Y	probably benign	Het
Ercc3	A	G	18: 32,248,429	T433A	probably benign	Het
Gm9936	T	A	5: 114,857,421		probably benign	Het
Grina	T	C	15: 76,248,534	V167A	probably damaging	Het
Hcfc2	A	G	10: 82,738,980	N618D	probably benign	Het
Herpud1	T	C	8: 94,392,206	V196A	probably benign	Het
Hist3h2a	T	A	11: 58,954,928	L64Q	probably damaging	Het
Hlcs	A	G	16: 94,262,740	V487A	probably benign	Het
Hspa9	A	T	18: 34,946,648	Y243N	probably damaging	Het
Igll1	A	G	16: 16,863,775	S39P	probably benign	Het
Kdm5a	T	C	6: 120,431,990	S1545P	probably benign	Het
Klra8	C	A	6: 130,115,573	C255F	probably damaging	Het
Krtap4-6	A	T	11: 99,665,572	C110S	unknown	Het
Lef1	T	A	3: 131,111,587	I39N	probably damaging	Het
Lnpep	G	A	17: 17,579,063	T110I	probably damaging	Het
Lrp1	T	A	10: 127,540,694	T4282S	probably benign	Het
Lrp6	A	G	6: 134,480,374		probably null	Het
Ly6g5b	A	C	17: 35,114,678	S53A	possibly damaging	Het
M6pr	T	G	6: 122,313,373	N98K	probably damaging	Het
Mal2	T	C	15: 54,600,740	*176Q	probably null	Het
Mansc1	T	C	6: 134,610,311	D301G	possibly damaging	Het
March1	C	A	8: 66,121,821	N11K	probably damaging	Het
Mast3	T	A	8: 70,787,363	I338F	probably benign	Het
Mcm3	A	G	1: 20,803,580	L772P	probably damaging	Het
Mib2	C	T	4: 155,657,880	G176D	probably damaging	Het
Mier2	A	T	10: 79,541,202		probably null	Het
Mogs	C	T	6: 83,117,650	R483*	probably null	Het
Msl2	G	T	9: 101,075,251		probably benign	Het
Naa16	A	T	14: 79,345,059	M530K	probably damaging	Het
Ndufb10	T	C	17: 24,722,529		probably null	Het
Nhsl1	A	T	10: 18,511,592	R205W	probably damaging	Het
Npffr2	T	A	5: 89,582,892	I227N	probably damaging	Het
Nup210l	T	A	3: 90,185,432	L1231Q	probably damaging	Het
Olfr1355	T	C	10: 78,879,388	I72T	possibly damaging	Het
Olfr453	A	G	6: 42,744,850	E271G	probably damaging	Het
Pclo	C	A	5: 14,521,501	P300Q	probably damaging	Het
Pik3c2a	T	A	7: 116,350,931		probably null	Het
Plekha5	T	A	6: 140,534,564		probably null	Het
Pls1	A	G	9: 95,761,365	V527A	possibly damaging	Het
Ppfia2	T	C	10: 106,474,677	M15T	probably benign	Het
Prkd2	T	A	7: 16,847,677	C152*	probably null	Het
Ptprq	T	G	10: 107,667,422	K792Q	probably damaging	Het
Rbbp8	T	C	18: 11,720,624	M296T	probably benign	Het
Rfc3	T	C	5: 151,647,538		probably null	Het
Rnf17	A	G	14: 56,486,969	N1090S	probably benign	Het
Sash1	A	T	10: 8,729,413	V1071D	probably benign	Het
Sdsl	G	A	5: 120,463,153	T18M	probably damaging	Het
Sepsecs	T	A	5: 52,647,624	Q365L	probably benign	Het
Sgta	A	T	10: 81,051,296	V45E	probably damaging	Het
Slc25a46	A	T	18: 31,609,725	H29Q	probably benign	Het
Slc2a8	A	C	2: 32,981,380	V136G	probably benign	Het
Smg7	A	T	1: 152,860,508	N166K	probably damaging	Het
Spata21	C	T	4: 141,107,329	Q505*	probably null	Het
Strn4	T	C	7: 16,833,028	S458P	possibly damaging	Het
Tbc1d22a	C	T	15: 86,299,684	T248M	probably damaging	Het
Trabd	T	A	15: 89,084,726	M149K	possibly damaging	Het
Trpv3	A	T	11: 73,279,827	N178Y	probably damaging	Het
Try5	C	T	6: 41,314,651		probably null	Het
Tsg101	C	T	7: 46,908,904		probably null	Het
Ube3b	A	G	5: 114,411,149	E738G	probably damaging	Het
Unc13d	A	G	11: 116,068,755	S631P	probably damaging	Het
Unc5d	T	C	8: 28,758,979	T297A	probably damaging	Het
Usp18	A	T	6: 121,268,550	E1V	probably damaging	Het
Vapb	C	A	2: 173,771,598	P97T	probably benign	Het
Vmn1r33	T	A	6: 66,612,372	D66V	probably benign	Het
Vmn2r19	T	A	6: 123,315,995	M332K	probably benign	Het
Vmn2r71	T	A	7: 85,620,637	M452K	probably benign	Het
Vps13b	T	C	15: 35,607,142	S1074P	probably damaging	Het
Vwde	C	A	6: 13,208,338	G182C	possibly damaging	Het
Wdfy3	A	C	5: 101,860,486	S2778A	probably null	Het
Zbtb2	T	A	10: 4,369,757	I90F	possibly damaging	Het
Zfp518b	C	A	5: 38,672,002	V887F	probably benign	Het
Zfp790	A	G	7: 29,828,861	T324A	probably benign	Het
Zufsp	A	G	10: 33,929,824	V437A	possibly damaging	Het

Other mutations in Nde1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03013:Nde1	APN	16	14191747	missense	probably benign
A4554:Nde1	UTSW	16	14188410	splice site	probably benign
PIT4515001:Nde1	UTSW	16	14170493	critical splice donor site	probably null
R1473:Nde1	UTSW	16	14185864	missense	probably benign	0.07
R2014:Nde1	UTSW	16	14169457	start gained	probably benign
R4426:Nde1	UTSW	16	14188336	missense	possibly damaging	0.94
R5116:Nde1	UTSW	16	14183487	missense	probably benign	0.19
R5646:Nde1	UTSW	16	14169514	missense	probably damaging	1.00
R6770:Nde1	UTSW	16	14188378	missense	probably damaging	1.00
R7722:Nde1	UTSW	16	14190264	missense	unknown
R8856:Nde1	UTSW	16	14183582	missense
R9405:Nde1	UTSW	16	14188391	missense	probably damaging	1.00
R9574:Nde1	UTSW	16	14170481	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TGGATCTAAGGGCTAGGTACTAAGTG -3'
(R):5'- TCATCTCACGGTAAGGCTGC -3'

Sequencing Primer
(F):5'- GTTTGTGGGGAGATATACATAAGCCC -3'
(R):5'- TCTCACGGTAAGGCTGCATTCG -3'

Posted On

2014-08-25