Mutagenetix > Incidental Mutation

Incidental Mutation 'R4126:Nid1'

315412

Institutional Source

Beutler Lab

Gene Symbol

Nid1

Ensembl Gene

ENSMUSG00000005397

Gene Name

nidogen 1

Synonyms

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

MMRRC Submission

041634-MU

Accession Numbers

Essential gene?

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

Stock #

R4126 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13612252-13686849 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 13650957 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 498 (V498A)

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: V498A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: V498A

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

0.3502

Coding Region Coverage

1x: 99.5%
3x: 98.7%
10x: 97.3%
20x: 95.2%

Validation Efficiency

89% (33/37)

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: 30 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadat	T	A	8: 60,984,703 (GRCm39)	W249R	probably benign	Het
Ank	G	A	15: 27,590,459 (GRCm39)	V348I	probably benign	Het
Atad3a	A	T	4: 155,838,518 (GRCm39)		probably benign	Het
Bbox1	A	G	2: 110,100,525 (GRCm39)	V224A	probably benign	Het
Cdk5rap1	A	G	2: 154,210,815 (GRCm39)	C108R	probably damaging	Het
Cds2	A	G	2: 132,139,191 (GRCm39)	T145A	probably benign	Het
Celsr2	G	T	3: 108,309,413 (GRCm39)	A1614D	possibly damaging	Het
Chd9	A	G	8: 91,777,912 (GRCm39)	D2641G	probably damaging	Het
E2f8	T	C	7: 48,525,355 (GRCm39)	I206V	probably damaging	Het
Glyat	G	T	19: 12,628,843 (GRCm39)	V213F	probably benign	Het
Gpatch1	C	T	7: 34,993,079 (GRCm39)		probably null	Het
Jarid2	T	C	13: 45,055,732 (GRCm39)	S313P	probably damaging	Het
Kcnc1	T	C	7: 46,047,426 (GRCm39)	Y109H	probably damaging	Het
Kif12	C	T	4: 63,084,674 (GRCm39)	S548N	probably benign	Het
Muc6	G	A	7: 141,218,313 (GRCm39)	S2120F	possibly damaging	Het
Myrip	C	A	9: 120,293,764 (GRCm39)	S753*	probably null	Het
Naalad2	T	C	9: 18,258,766 (GRCm39)	Y503C	probably damaging	Het
Or8k25	A	T	2: 86,243,568 (GRCm39)	I276N	probably damaging	Het
Parp8	C	A	13: 117,005,005 (GRCm39)	K685N	possibly damaging	Het
Prr14l	G	T	5: 32,985,347 (GRCm39)	H1383N	probably damaging	Het
Pxn	A	G	5: 115,684,966 (GRCm39)	R264G	probably damaging	Het
Slc6a20a	G	T	9: 123,489,598 (GRCm39)	F148L	probably damaging	Het
Spag11b	T	C	8: 19,191,395 (GRCm39)	S23P	possibly damaging	Het
Stac	C	A	9: 111,433,126 (GRCm39)		probably null	Het
Taf11	T	C	17: 28,120,746 (GRCm39)	K175E	possibly damaging	Het
Tll1	T	C	8: 64,571,048 (GRCm39)	R175G	possibly damaging	Het
Trip11	G	A	12: 101,861,957 (GRCm39)	Q203*	probably null	Het
Usp4	T	C	9: 108,237,316 (GRCm39)	V128A	probably benign	Het
Zfp788	T	C	7: 41,298,860 (GRCm39)	F479L	probably damaging	Het
Zmiz1	T	G	14: 25,657,354 (GRCm39)	S877A	possibly 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
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'- CTCTCCACAACGGGTCAATG -3'
(R):5'- TGGTCCTTATTTCTGAGGAAGAAC -3'

Sequencing Primer
(F):5'- CCACAACGGGTCAATGGCAAG -3'
(R):5'- AAGAACTAGAGGGCCCCTGTC -3'

Posted On

2015-05-14