Mutagenetix > Incidental Mutation

Incidental Mutation 'R4834:Nid1'

373091

Institutional Source

Beutler Lab

Gene Symbol

Nid1

Ensembl Gene

ENSMUSG00000005397

Gene Name

nidogen 1

Synonyms

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

MMRRC Submission

041977-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.202) question?

Stock #

R4834 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

13612252-13686849 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13683408 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 1162 (Y1162C)

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: Y1162C

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

SMART Domains

Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: Y1162C

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: ENSMUST00000222436

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

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 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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930550C14Rik	A	C	9: 53,343,787 (GRCm39)	D146A	possibly damaging	Het
Acsl5	C	A	19: 55,268,991 (GRCm39)	D217E	probably benign	Het
Acss3	A	G	10: 106,920,666 (GRCm39)		probably null	Het
Adam24	G	A	8: 41,132,738 (GRCm39)	G69R	probably damaging	Het
Adgrg7	A	T	16: 56,553,232 (GRCm39)	W622R	probably damaging	Het
Ajm1	T	C	2: 25,469,530 (GRCm39)	E127G	possibly damaging	Het
Ankrd26	T	C	6: 118,500,679 (GRCm39)	M931V	probably benign	Het
Ano8	C	T	8: 71,936,939 (GRCm39)	V187M	probably damaging	Het
Ap3d1	A	T	10: 80,555,560 (GRCm39)	C348S	probably damaging	Het
Apob	T	C	12: 8,064,101 (GRCm39)	V376A	possibly damaging	Het
Arhgap21	A	T	2: 20,870,130 (GRCm39)	D925E	probably damaging	Het
Bmp6	T	A	13: 38,669,817 (GRCm39)	V367E	probably damaging	Het
Bmp8b	A	T	4: 123,016,843 (GRCm39)	Q348L	probably damaging	Het
Ccr1l1	T	C	9: 123,777,742 (GRCm39)	K235R	probably damaging	Het
Cd59a	G	A	2: 103,944,431 (GRCm39)	C93Y	probably damaging	Het
Clstn3	C	T	6: 124,408,912 (GRCm39)		probably null	Het
Col4a2	C	A	8: 11,456,836 (GRCm39)	Y236*	probably null	Het
Csn1s2a	T	C	5: 87,929,637 (GRCm39)	F79L	probably benign	Het
Cyp4a10	A	C	4: 115,383,005 (GRCm39)	Y360S	probably damaging	Het
Cyp4a29	A	T	4: 115,106,867 (GRCm39)	I175F	probably benign	Het
Dck	T	A	5: 88,920,595 (GRCm39)	I105N	probably damaging	Het
Dicer1	A	G	12: 104,662,850 (GRCm39)	L1577P	probably benign	Het
Disp2	G	A	2: 118,622,985 (GRCm39)	S1239N	probably benign	Het
Dop1b	T	C	16: 93,536,892 (GRCm39)	M1T	probably null	Het
E130308A19Rik	T	A	4: 59,690,317 (GRCm39)	C50*	probably null	Het
Elf2	A	T	3: 51,184,642 (GRCm39)	D14E	probably damaging	Het
Epm2aip1	C	T	9: 111,102,262 (GRCm39)	R412C	probably benign	Het
Foxm1	T	C	6: 128,346,410 (GRCm39)	F114L	probably damaging	Het
Glcci1	C	T	6: 8,582,601 (GRCm39)	R134*	probably null	Het
Gm57859	C	A	11: 113,579,805 (GRCm39)	T400K	probably benign	Het
Gspt1	T	C	16: 11,040,581 (GRCm39)	K576E	probably damaging	Het
H2-M10.3	T	C	17: 36,678,286 (GRCm39)	K180E	probably benign	Het
Hecw2	A	T	1: 53,869,911 (GRCm39)	V1439E	probably damaging	Het
Hr	T	C	14: 70,797,362 (GRCm39)	S561P	probably damaging	Het
Hunk	T	C	16: 90,293,086 (GRCm39)	V456A	probably benign	Het
Il1rap	T	A	16: 26,495,685 (GRCm39)	D97E	probably damaging	Het
Inpp5d	T	G	1: 87,625,245 (GRCm39)	V474G	possibly damaging	Het
Itsn1	T	A	16: 91,703,677 (GRCm39)	L87*	probably null	Het
Izumo3	T	C	4: 92,035,208 (GRCm39)	D3G	possibly damaging	Het
Kifc2	T	A	15: 76,545,511 (GRCm39)	M1K	probably null	Het
Krt8	T	A	15: 101,907,256 (GRCm39)	I276F	probably damaging	Het
Ksr2	C	A	5: 117,806,392 (GRCm39)	Q402K	probably benign	Het
Lama2	A	G	10: 26,882,745 (GRCm39)	V2606A	probably benign	Het
Met	A	G	6: 17,491,412 (GRCm39)	H58R	probably damaging	Het
Mier3	C	T	13: 111,851,643 (GRCm39)	Q542*	probably null	Het
Msh2	C	A	17: 88,030,841 (GRCm39)	A906E	probably benign	Het
Msl3l2	C	T	10: 55,991,655 (GRCm39)	R127C	probably damaging	Het
Naglu	T	C	11: 100,967,814 (GRCm39)	L588P	probably benign	Het
Nf1	T	C	11: 79,437,123 (GRCm39)	L2013P	probably damaging	Het
Nlrc5	G	T	8: 95,232,113 (GRCm39)	R1313L	probably benign	Het
Nrg1	A	G	8: 32,407,747 (GRCm39)	V162A	probably benign	Het
Nup188	T	C	2: 30,229,596 (GRCm39)	L1310P	probably damaging	Het
Ofcc1	G	A	13: 40,168,864 (GRCm39)	T841I	probably damaging	Het
Or14a259	G	A	7: 86,012,952 (GRCm39)	L198F	probably benign	Het
Or4f6	A	G	2: 111,839,276 (GRCm39)	L85P	probably damaging	Het
Or5ae1	T	G	7: 84,565,491 (GRCm39)	F168C	probably damaging	Het
Pbk	T	A	14: 66,052,733 (GRCm39)	L192*	probably null	Het
Pcdhga4	T	C	18: 37,818,490 (GRCm39)	I13T	probably benign	Het
Peg10	A	T	6: 4,754,294 (GRCm39)		probably benign	Het
Polq	T	A	16: 36,848,176 (GRCm39)	V261D	probably damaging	Het
Ppp2r5b	T	A	19: 6,280,540 (GRCm39)	T313S	possibly damaging	Het
Ptk2	A	T	15: 73,087,945 (GRCm39)		probably null	Het
Ptpn7	T	A	1: 135,065,618 (GRCm39)		probably null	Het
Rab11fip1	A	G	8: 27,643,111 (GRCm39)	S563P	probably damaging	Het
Scn1a	A	T	2: 66,158,866 (GRCm39)	C351*	probably null	Het
Slc10a5	A	T	3: 10,399,859 (GRCm39)	V267D	probably damaging	Het
Slc37a2	T	A	9: 37,146,404 (GRCm39)	M368L	probably damaging	Het
Slc49a4	T	A	16: 35,555,945 (GRCm39)	T172S	probably benign	Het
Slc6a20b	T	A	9: 123,425,113 (GRCm39)	T585S	probably benign	Het
Srcap	T	C	7: 127,156,782 (GRCm39)		probably null	Het
Tbx18	T	C	9: 87,609,502 (GRCm39)	M178V	possibly damaging	Het
Tmprss11b	C	A	5: 86,811,418 (GRCm39)	C172F	probably damaging	Het
Traf5	T	C	1: 191,751,198 (GRCm39)	Q91R	probably benign	Het
Trappc8	A	T	18: 20,958,122 (GRCm39)	Y1248N	probably damaging	Het
Trpa1	A	G	1: 14,966,747 (GRCm39)	L539S	possibly damaging	Het
Tyrp1	T	A	4: 80,764,833 (GRCm39)	Y3*	probably null	Het
Ubr7	A	T	12: 102,727,761 (GRCm39)	K94N	probably damaging	Het
Ugt2a1	C	A	5: 87,633,894 (GRCm39)		probably null	Het
Unc50	T	A	1: 37,471,710 (GRCm39)	I120K	probably damaging	Het
Usp28	T	C	9: 48,912,836 (GRCm39)	V29A	probably damaging	Het
Usp9y	A	G	Y: 1,317,002 (GRCm39)	I1849T	probably benign	Het
Vmn2r102	T	A	17: 19,898,203 (GRCm39)	V406E	probably damaging	Het
Vmn2r4	G	A	3: 64,317,484 (GRCm39)	R85W	probably benign	Het
Xirp2	A	G	2: 67,346,750 (GRCm39)	D2997G	probably benign	Het
Zc2hc1c	A	T	12: 85,336,982 (GRCm39)	E213V	probably damaging	Het
Zfp420	C	T	7: 29,573,759 (GRCm39)		probably benign	Het
Zfp641	C	T	15: 98,191,585 (GRCm39)	E34K	probably damaging	Het

Other mutations in Nid1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00092:Nid1	APN	13	13,650,977 (GRCm39)	missense	probably damaging	1.00
IGL02126:Nid1	APN	13	13,663,743 (GRCm39)	splice site	probably null
IGL02452:Nid1	APN	13	13,683,305 (GRCm39)	missense	probably benign	0.17
IGL02806:Nid1	APN	13	13,642,897 (GRCm39)	missense	probably benign	0.00
IGL02966:Nid1	APN	13	13,656,806 (GRCm39)	missense	probably benign	0.09
IGL03136:Nid1	APN	13	13,675,084 (GRCm39)	missense	probably benign	0.33
IGL03411:Nid1	APN	13	13,612,474 (GRCm39)	missense	probably damaging	0.98
R0384:Nid1	UTSW	13	13,638,421 (GRCm39)	missense	probably benign	0.34
R0413:Nid1	UTSW	13	13,656,681 (GRCm39)	missense	probably benign	0.01
R1257:Nid1	UTSW	13	13,658,375 (GRCm39)	missense	probably benign	0.01
R1390:Nid1	UTSW	13	13,650,831 (GRCm39)	missense	probably damaging	1.00
R1397:Nid1	UTSW	13	13,683,380 (GRCm39)	missense	possibly damaging	0.94
R2057:Nid1	UTSW	13	13,675,058 (GRCm39)	missense	probably benign	0.00
R2058:Nid1	UTSW	13	13,675,058 (GRCm39)	missense	probably benign	0.00
R2059:Nid1	UTSW	13	13,675,058 (GRCm39)	missense	probably benign	0.00
R2132:Nid1	UTSW	13	13,684,071 (GRCm39)	missense	probably benign	0.04
R2140:Nid1	UTSW	13	13,674,253 (GRCm39)	missense	probably damaging	1.00
R2195:Nid1	UTSW	13	13,650,788 (GRCm39)	missense	probably damaging	1.00
R2237:Nid1	UTSW	13	13,675,070 (GRCm39)	missense	probably benign
R2312:Nid1	UTSW	13	13,675,078 (GRCm39)	missense	probably benign	0.15
R2987:Nid1	UTSW	13	13,674,258 (GRCm39)	missense	probably benign	0.40
R3696:Nid1	UTSW	13	13,661,344 (GRCm39)	missense	probably damaging	0.99
R3697:Nid1	UTSW	13	13,661,344 (GRCm39)	missense	probably damaging	0.99
R3698:Nid1	UTSW	13	13,661,344 (GRCm39)	missense	probably damaging	0.99
R3772:Nid1	UTSW	13	13,651,003 (GRCm39)	splice site	probably benign
R4092:Nid1	UTSW	13	13,661,224 (GRCm39)	missense	probably damaging	0.96
R4126:Nid1	UTSW	13	13,650,957 (GRCm39)	missense	probably damaging	1.00
R4128:Nid1	UTSW	13	13,650,957 (GRCm39)	missense	probably damaging	1.00
R4680:Nid1	UTSW	13	13,647,437 (GRCm39)	missense	probably damaging	1.00
R4717:Nid1	UTSW	13	13,681,086 (GRCm39)	missense	probably benign	0.00
R4783:Nid1	UTSW	13	13,674,326 (GRCm39)	missense	probably damaging	0.97
R4812:Nid1	UTSW	13	13,681,053 (GRCm39)	nonsense	probably null
R4915:Nid1	UTSW	13	13,674,171 (GRCm39)	missense	possibly damaging	0.89
R4930:Nid1	UTSW	13	13,684,596 (GRCm39)	missense	probably damaging	1.00
R5101:Nid1	UTSW	13	13,658,339 (GRCm39)	missense	probably damaging	1.00
R5276:Nid1	UTSW	13	13,643,157 (GRCm39)	missense	probably damaging	0.99
R5427:Nid1	UTSW	13	13,658,268 (GRCm39)	missense	probably damaging	1.00
R5447:Nid1	UTSW	13	13,612,495 (GRCm39)	missense	probably benign	0.00
R5507:Nid1	UTSW	13	13,663,622 (GRCm39)	nonsense	probably null
R5663:Nid1	UTSW	13	13,647,419 (GRCm39)	missense	probably damaging	1.00
R5868:Nid1	UTSW	13	13,663,742 (GRCm39)	critical splice donor site	probably null
R6313:Nid1	UTSW	13	13,638,367 (GRCm39)	missense	probably benign	0.01
R6761:Nid1	UTSW	13	13,656,620 (GRCm39)	missense	probably benign	0.22
R7069:Nid1	UTSW	13	13,683,353 (GRCm39)	missense	probably benign
R7208:Nid1	UTSW	13	13,642,970 (GRCm39)	missense	probably benign	0.01
R7284:Nid1	UTSW	13	13,663,675 (GRCm39)	missense	probably benign	0.01
R7434:Nid1	UTSW	13	13,643,049 (GRCm39)	missense	probably benign
R7449:Nid1	UTSW	13	13,656,636 (GRCm39)	missense	probably damaging	1.00
R7574:Nid1	UTSW	13	13,643,028 (GRCm39)	missense	probably benign
R7762:Nid1	UTSW	13	13,663,630 (GRCm39)	missense	probably damaging	1.00
R7887:Nid1	UTSW	13	13,674,318 (GRCm39)	missense	possibly damaging	0.83
R8420:Nid1	UTSW	13	13,612,416 (GRCm39)	missense	possibly damaging	0.81
R8506:Nid1	UTSW	13	13,650,759 (GRCm39)	missense	probably damaging	0.99
R8756:Nid1	UTSW	13	13,683,386 (GRCm39)	missense	probably benign	0.32
R8903:Nid1	UTSW	13	13,638,515 (GRCm39)	missense	probably benign	0.00
R9084:Nid1	UTSW	13	13,652,925 (GRCm39)	critical splice donor site	probably null
R9297:Nid1	UTSW	13	13,650,897 (GRCm39)	missense	possibly damaging	0.92
R9344:Nid1	UTSW	13	13,652,894 (GRCm39)	missense	probably damaging	1.00
R9552:Nid1	UTSW	13	13,677,045 (GRCm39)	missense	probably damaging	0.99
X0028:Nid1	UTSW	13	13,684,119 (GRCm39)	missense	probably benign	0.14

Predicted Primers

PCR Primer
(F):5'- CTCCAGGACATGCCATTGAAAC -3'
(R):5'- AGATTAGACAGCCCTCTTCCTC -3'

Sequencing Primer
(F):5'- GGACATGCCATTGAAACACTGAATTC -3'
(R):5'- CTACCCTCCTCCATATCTGACAG -3'

Posted On

2016-03-01