Mutagenetix > Incidental Mutation

Incidental Mutation 'R2140:Nid1'

236155

Institutional Source

Beutler Lab

Gene Symbol

Nid1

Ensembl Gene

ENSMUSG00000005397

Gene Name

nidogen 1

Synonyms

entactin 1, nidogen-1, entactin, entactin-1

MMRRC Submission

040143-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.269) question?

Stock #

R2140 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13437551-13512269 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 13499668 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 877 (D877E)

Ref Sequence

ENSEMBL: ENSMUSP00000005532 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005532]

AlphaFold

P10493

PDB Structure

NIDOGEN-1 G2/PERLECAN IG3 COMPLEX [X-RAY DIFFRACTION]
DOMAIN G2 OF MOUSE NIDOGEN-1 [X-RAY DIFFRACTION]
Crystal structure of Nidogen/Laminin Complex [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000005532
AA Change: D877E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: D877E

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
NIDO	106	270	3.8e-70	SMART
low complexity region	277	296	N/A	INTRINSIC
EGF	387	424	3.46e0	SMART
G2F	425	664	7.69e-153	SMART
EGF	669	707	8.65e-1	SMART
EGF_CA	708	749	4.38e-11	SMART
EGF	759	799	8.19e-2	SMART
EGF_CA	800	838	1.42e-10	SMART
TY	873	921	1.17e-19	SMART
LY	968	1010	1.35e-2	SMART
LY	1011	1053	4.34e-15	SMART
LY	1054	1098	3.34e-16	SMART
LY	1099	1141	3.25e-5	SMART
LY	1142	1181	1.08e1	SMART
EGF	1209	1242	2.45e0	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000222142

Meta Mutation Damage Score

0.1656

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.5%

Validation Efficiency

100% (96/96)

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 nidogen family of basement membrane glycoproteins. The protein interacts with several other components of basement membranes, and may play a role in cell interactions with the extracellular matrix. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neurologic deficits including seizure-like symptoms and loss of muscle control in the hind legs, and show altered basement membrane morphology in selected locations including brain capillaries and the lens capsule. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610042L04Rik	T	C	14: 4,348,902	I21T	probably damaging	Het
9230110C19Rik	T	C	9: 8,022,477	D248G	probably damaging	Het
Adgrf1	A	C	17: 43,300,802	E186D	probably damaging	Het
Adgrf4	C	T	17: 42,666,898	R518Q	possibly damaging	Het
Afdn	A	G	17: 13,810,433	E202G	probably damaging	Het
Agfg2	T	A	5: 137,667,116	R126W	probably damaging	Het
Alkbh2	C	T	5: 114,125,716	V77I	probably benign	Het
Alppl2	A	G	1: 87,087,697	S381P	probably benign	Het
Aqp2	A	G	15: 99,579,366	T72A	probably damaging	Het
Atp9b	A	G	18: 80,736,087	C1123R	probably damaging	Het
AU016765	T	A	17: 64,520,000		noncoding transcript	Het
Bscl2	T	C	19: 8,845,320		probably null	Het
Ccdc80	A	T	16: 45,127,446	Y929F	probably damaging	Het
Cenpj	T	C	14: 56,526,932	D1341G	probably damaging	Het
Cir1	A	T	2: 73,312,437	S18T	probably damaging	Het
Clcn6	A	G	4: 148,024,137	F145S	possibly damaging	Het
Cnksr1	A	G	4: 134,229,628	Y488H	probably damaging	Het
Cntrl	CAGAG	CAG	2: 35,122,806		probably null	Het
Crb1	T	C	1: 139,237,012	I1125V	probably benign	Het
Cyp3a13	A	T	5: 137,921,454	V20D	possibly damaging	Het
Dars	T	A	1: 128,372,162	M362L	probably benign	Het
Dck	T	C	5: 88,772,723	C101R	probably damaging	Het
Dnah11	T	C	12: 118,008,810	T2880A	probably benign	Het
Dnah7b	T	A	1: 46,268,670	M3048K	probably damaging	Het
Eef1a2	C	T	2: 181,148,742	E374K	probably benign	Het
Eif3a	A	T	19: 60,775,394		probably benign	Het
Esco1	A	G	18: 10,574,873		probably null	Het
Exoc8	C	T	8: 124,897,415	R71Q	possibly damaging	Het
Fam208a	C	T	14: 27,480,035	T1462I	probably damaging	Het
Far1	G	A	7: 113,566,460	V445M	possibly damaging	Het
Fbn1	C	A	2: 125,343,810	C1648F	probably damaging	Het
Fmn1	A	G	2: 113,595,048	K1189R	probably benign	Het
Foxl2	C	A	9: 98,956,487	P276H	unknown	Het
Fpr3	T	A	17: 17,970,617	V50E	probably damaging	Het
Garem1	T	A	18: 21,129,374	R794S	probably damaging	Het
Gemin4	G	C	11: 76,211,050	P962A	probably damaging	Het
Glyatl3	T	C	17: 40,911,084	D93G	probably benign	Het
Gm14124	A	T	2: 150,269,361	H657L	probably benign	Het
Gm4787	A	G	12: 81,378,562	I274T	probably benign	Het
Gucy1a1	C	T	3: 82,118,886		probably null	Het
Hook1	GATGAATGA	GATGA	4: 96,013,312	503	probably null	Het
Ift20	G	A	11: 78,540,034	E68K	probably damaging	Het
Ints13	A	G	6: 146,576,431	S7P	probably damaging	Het
Kat5	T	A	19: 5,605,685		probably null	Het
Kcnma1	A	C	14: 23,314,220	L988R	probably damaging	Het
Kcnq3	C	A	15: 66,005,978		probably benign	Het
Kctd16	A	G	18: 40,259,178	E273G	possibly damaging	Het
Krt82	T	A	15: 101,545,156	Q265L	probably damaging	Het
Lama2	A	T	10: 27,054,694		probably null	Het
Laptm4b	G	T	15: 34,238,332	M3I	probably benign	Het
Lmtk2	A	G	5: 144,147,615	Y156C	probably damaging	Het
Lrrc58	G	A	16: 37,881,409	E350K	probably damaging	Het
Lrrk1	A	T	7: 66,330,750	D227E	probably damaging	Het
Macf1	C	T	4: 123,355,102	C7210Y	probably damaging	Het
Madd	A	G	2: 91,152,509	I1363T	possibly damaging	Het
Mcm3	A	G	1: 20,813,110	V295A	probably benign	Het
Mki67	A	G	7: 135,695,592	I2571T	possibly damaging	Het
Mtrr	C	T	13: 68,568,940	A385T	possibly damaging	Het
Myh7b	A	G	2: 155,620,123	Y313C	probably damaging	Het
Myot	A	T	18: 44,354,125	H343L	possibly damaging	Het
Myt1	C	A	2: 181,825,979	Q1069K	probably damaging	Het
Nle1	A	G	11: 82,905,568	V159A	probably damaging	Het
Nmbr	C	A	10: 14,770,442	Y353*	probably null	Het
Nos1ap	T	A	1: 170,329,166	D241V	probably damaging	Het
Nostrin	A	C	2: 69,166,003	Y209S	probably damaging	Het
Olfr1099	A	T	2: 86,959,281	M59K	probably damaging	Het
Olfr115	T	G	17: 37,610,471	E93D	probably benign	Het
Olfr1168	A	T	2: 88,185,095	S73C	probably benign	Het
Olfr1240	C	T	2: 89,439,583	R232H	probably benign	Het
Olfr283	G	A	15: 98,378,396	T238I	possibly damaging	Het
Olfr378	A	T	11: 73,425,881	M34K	probably damaging	Het
Pcdh7	T	A	5: 58,128,996	V1138E	probably damaging	Het
Pglyrp3	T	G	3: 92,026,567	V173G	probably benign	Het
Plec	T	C	15: 76,183,174	T1331A	probably benign	Het
Plxnb2	T	C	15: 89,156,562	D1787G	probably benign	Het
Pms1	T	A	1: 53,281,988	I29F	probably damaging	Het
Ptprt	G	A	2: 161,811,988	T574I	probably damaging	Het
R3hdm1	A	G	1: 128,190,693	Y561C	probably damaging	Het
Rab17	A	G	1: 90,960,078	F120S	probably benign	Het
Rab7b	T	A	1: 131,698,419	W62R	probably damaging	Het
Ryr2	C	T	13: 11,560,607	G4835E	probably damaging	Het
Ryr3	A	G	2: 112,875,148	V807A	probably benign	Het
Sept4	A	T	11: 87,583,436	Q60L	probably benign	Het
Slc23a1	C	T	18: 35,626,434	R26Q	unknown	Het
Slc7a4	C	A	16: 17,574,544	R342L	possibly damaging	Het
Slfn9	C	T	11: 82,984,655	C367Y	possibly damaging	Het
Slitrk6	T	G	14: 110,750,794	T494P	probably benign	Het
Tiam1	A	G	16: 89,849,645		probably benign	Het
Tiparp	C	A	3: 65,529,252		probably benign	Het
Tmem39b	T	C	4: 129,678,688	T374A	probably benign	Het
Trim5	G	A	7: 104,276,791	R188*	probably null	Het
Ttn	C	T	2: 76,813,339	G11436R	probably damaging	Het
Ubr4	C	T	4: 139,477,207	T4810M	probably damaging	Het
Vmn2r26	A	T	6: 124,061,237	E590D	probably benign	Het
Wwc1	A	G	11: 35,870,528	F650S	probably benign	Het
Xrcc6	T	A	15: 82,022,977	F167I	probably damaging	Het

Other mutations in Nid1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00092:Nid1	APN	13	13476392	missense	probably damaging	1.00
IGL02126:Nid1	APN	13	13489158	splice site	probably null
IGL02452:Nid1	APN	13	13508720	missense	probably benign	0.17
IGL02806:Nid1	APN	13	13468312	missense	probably benign	0.00
IGL02966:Nid1	APN	13	13482221	missense	probably benign	0.09
IGL03136:Nid1	APN	13	13500499	missense	probably benign	0.33
IGL03411:Nid1	APN	13	13437889	missense	probably damaging	0.98
R0384:Nid1	UTSW	13	13463836	missense	probably benign	0.34
R0413:Nid1	UTSW	13	13482096	missense	probably benign	0.01
R1257:Nid1	UTSW	13	13483790	missense	probably benign	0.01
R1390:Nid1	UTSW	13	13476246	missense	probably damaging	1.00
R1397:Nid1	UTSW	13	13508795	missense	possibly damaging	0.94
R2057:Nid1	UTSW	13	13500473	missense	probably benign	0.00
R2058:Nid1	UTSW	13	13500473	missense	probably benign	0.00
R2059:Nid1	UTSW	13	13500473	missense	probably benign	0.00
R2132:Nid1	UTSW	13	13509486	missense	probably benign	0.04
R2195:Nid1	UTSW	13	13476203	missense	probably damaging	1.00
R2237:Nid1	UTSW	13	13500485	missense	probably benign
R2312:Nid1	UTSW	13	13500493	missense	probably benign	0.15
R2987:Nid1	UTSW	13	13499673	missense	probably benign	0.40
R3696:Nid1	UTSW	13	13486759	missense	probably damaging	0.99
R3697:Nid1	UTSW	13	13486759	missense	probably damaging	0.99
R3698:Nid1	UTSW	13	13486759	missense	probably damaging	0.99
R3772:Nid1	UTSW	13	13476418	splice site	probably benign
R4092:Nid1	UTSW	13	13486639	missense	probably damaging	0.96
R4126:Nid1	UTSW	13	13476372	missense	probably damaging	1.00
R4128:Nid1	UTSW	13	13476372	missense	probably damaging	1.00
R4680:Nid1	UTSW	13	13472852	missense	probably damaging	1.00
R4717:Nid1	UTSW	13	13506501	missense	probably benign	0.00
R4783:Nid1	UTSW	13	13499741	missense	probably damaging	0.97
R4812:Nid1	UTSW	13	13506468	nonsense	probably null
R4834:Nid1	UTSW	13	13508823	missense	probably damaging	1.00
R4915:Nid1	UTSW	13	13499586	missense	possibly damaging	0.89
R4930:Nid1	UTSW	13	13510011	missense	probably damaging	1.00
R5101:Nid1	UTSW	13	13483754	missense	probably damaging	1.00
R5276:Nid1	UTSW	13	13468572	missense	probably damaging	0.99
R5427:Nid1	UTSW	13	13483683	missense	probably damaging	1.00
R5447:Nid1	UTSW	13	13437910	missense	probably benign	0.00
R5507:Nid1	UTSW	13	13489037	nonsense	probably null
R5663:Nid1	UTSW	13	13472834	missense	probably damaging	1.00
R5868:Nid1	UTSW	13	13489157	critical splice donor site	probably null
R6313:Nid1	UTSW	13	13463782	missense	probably benign	0.01
R6761:Nid1	UTSW	13	13482035	missense	probably benign	0.22
R7069:Nid1	UTSW	13	13508768	missense	probably benign
R7208:Nid1	UTSW	13	13468385	missense	probably benign	0.01
R7284:Nid1	UTSW	13	13489090	missense	probably benign	0.01
R7434:Nid1	UTSW	13	13468464	missense	probably benign
R7449:Nid1	UTSW	13	13482051	missense	probably damaging	1.00
R7574:Nid1	UTSW	13	13468443	missense	probably benign
R7762:Nid1	UTSW	13	13489045	missense	probably damaging	1.00
R7887:Nid1	UTSW	13	13499733	missense	possibly damaging	0.83
R8420:Nid1	UTSW	13	13437831	missense	possibly damaging	0.81
R8506:Nid1	UTSW	13	13476174	missense	probably damaging	0.99
R8756:Nid1	UTSW	13	13508801	missense	probably benign	0.32
R8903:Nid1	UTSW	13	13463930	missense	probably benign	0.00
R9084:Nid1	UTSW	13	13478340	critical splice donor site	probably null
R9297:Nid1	UTSW	13	13476312	missense	possibly damaging	0.92
R9344:Nid1	UTSW	13	13478309	missense	probably damaging	1.00
R9552:Nid1	UTSW	13	13502460	missense	probably damaging	0.99
X0028:Nid1	UTSW	13	13509534	missense	probably benign	0.14

Predicted Primers

PCR Primer
(F):5'- AGTTTGACAAGTAGCATTTGGG -3'
(R):5'- CAGAAACATGACCACCTGGG -3'

Sequencing Primer
(F):5'- TTGACAAGTAGCATTTGGGAACACC -3'
(R):5'- TTGGGAGCATGTGAACAGAGACC -3'

Posted On

2014-10-01