Mutagenetix > Incidental Mutation

Incidental Mutation 'R3697:Nid1'

269867

Institutional Source

Beutler Lab

Gene Symbol

Nid1

Ensembl Gene

ENSMUSG00000005397

Gene Name

nidogen 1

Synonyms

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

MMRRC Submission

040691-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.227) question?

Stock #

R3697 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

13612252-13686849 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 13661344 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 748 (C748Y)

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: C748Y

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: C748Y

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: ENSMUST00000220813

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000222142

Meta Mutation Damage Score

0.9742

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

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: 28 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh4a1	A	G	4: 139,369,562 (GRCm39)	H371R	possibly damaging	Het
Arhgef4	A	G	1: 34,761,521 (GRCm39)	D259G	unknown	Het
Bckdk	C	A	7: 127,504,590 (GRCm39)	R105S	probably damaging	Het
Clcn3	T	C	8: 61,366,157 (GRCm39)	D805G	probably benign	Het
Cnmd	C	A	14: 79,875,421 (GRCm39)	R333L	probably damaging	Het
Col4a4	A	T	1: 82,518,958 (GRCm39)	I79N	unknown	Het
Emc1	T	G	4: 139,092,697 (GRCm39)	S546A	possibly damaging	Het
Ermard	T	C	17: 15,273,638 (GRCm39)	S408P	probably benign	Het
Gls	C	T	1: 52,238,923 (GRCm39)	M364I	possibly damaging	Het
Gm16380	A	G	9: 53,791,736 (GRCm39)		noncoding transcript	Het
Il12a	TCAC	TC	3: 68,605,320 (GRCm39)		probably null	Het
Il6st	T	G	13: 112,640,916 (GRCm39)	D897E	probably benign	Het
Itga3	T	C	11: 94,953,551 (GRCm39)	T233A	probably benign	Het
Kcnd3	C	T	3: 105,566,082 (GRCm39)	A421V	probably damaging	Het
Lemd3	CCCTCCTCCTCCTCCTCCTCC	CCCTCCTCCTCCTCCTCC	10: 120,814,432 (GRCm39)		probably benign	Het
Miga1	T	C	3: 152,028,073 (GRCm39)	N152S	probably damaging	Het
Nckipsd	G	A	9: 108,688,320 (GRCm39)	G83S	probably damaging	Het
Nedd4	T	C	9: 72,647,469 (GRCm39)	F728L	probably damaging	Het
Nop56	C	A	2: 130,119,507 (GRCm39)	N57K	probably damaging	Het
Nup205	A	G	6: 35,165,646 (GRCm39)	N197S	probably benign	Het
Pglyrp3	T	A	3: 91,935,481 (GRCm39)	C244S	probably damaging	Het
Rgs22	C	T	15: 36,100,038 (GRCm39)	V226I	probably benign	Het
Rtp3	T	A	9: 110,816,262 (GRCm39)	R96S	possibly damaging	Het
Serpinb8	A	T	1: 107,534,876 (GRCm39)	K316*	probably null	Het
Sp6	C	A	11: 96,912,580 (GRCm39)	P98T	possibly damaging	Het
Vmn1r15	A	T	6: 57,235,321 (GRCm39)	D63V	possibly damaging	Het
Vmn1r216	G	A	13: 23,283,849 (GRCm39)	W177*	probably null	Het
Zfp414	CAAACTCTTCCGA	CAAACTCTTCCGAAACTCTTCCGA	17: 33,849,551 (GRCm39)		probably null	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
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
R4834:Nid1	UTSW	13	13,683,408 (GRCm39)	missense	probably damaging	1.00
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'- GTGTGTCTTCAAATGGATCTCTTC -3'
(R):5'- CACTCTTTGATCCTGGCAGC -3'

Sequencing Primer
(F):5'- CAAATGGATCTCTTCTCTGAGGAG -3'
(R):5'- CCACGACTGTCTAAGGAGGTCTTC -3'

Posted On

2015-03-18