Incidental Mutation 'R6313:Nid1'
| ID |
510540 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nid1
|
| Ensembl Gene |
ENSMUSG00000005397 |
| Gene Name |
nidogen 1 |
| Synonyms |
nidogen-1, entactin, entactin 1, entactin-1 |
| MMRRC Submission |
044470-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.202)
|
| Stock # |
R6313 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
13612252-13686849 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 13638367 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 96
(T96A)
|
| 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 benign
Transcript: ENSMUST00000005532
AA Change: T96A
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: T96A
| 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 |
0.0898 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.4%
|
| Validation Efficiency |
100% (70/70) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca16 |
T |
C |
7: 120,126,344 (GRCm39) |
F1167L |
probably damaging |
Het |
| Abraxas2 |
G |
A |
7: 132,476,694 (GRCm39) |
A145T |
probably damaging |
Het |
| Acaca |
C |
T |
11: 84,183,755 (GRCm39) |
T32I |
probably benign |
Het |
| Adam6a |
A |
T |
12: 113,508,670 (GRCm39) |
N348Y |
possibly damaging |
Het |
| Ankdd1a |
C |
T |
9: 65,415,343 (GRCm39) |
A227T |
possibly damaging |
Het |
| Arhgef38 |
T |
C |
3: 132,940,469 (GRCm39) |
D39G |
possibly damaging |
Het |
| Arid5b |
T |
C |
10: 67,933,412 (GRCm39) |
D587G |
possibly damaging |
Het |
| Brwd1 |
A |
G |
16: 95,809,141 (GRCm39) |
V1963A |
probably benign |
Het |
| Ccdc136 |
T |
A |
6: 29,410,204 (GRCm39) |
L34Q |
probably damaging |
Het |
| Cdh2 |
T |
C |
18: 16,907,579 (GRCm39) |
Q53R |
probably benign |
Het |
| Celsr2 |
G |
A |
3: 108,308,530 (GRCm39) |
S1799L |
probably damaging |
Het |
| Cenpe |
A |
G |
3: 134,935,936 (GRCm39) |
E457G |
probably benign |
Het |
| Cmtm1 |
A |
T |
8: 105,031,795 (GRCm39) |
M283K |
possibly damaging |
Het |
| Dcdc5 |
T |
C |
2: 106,198,516 (GRCm39) |
|
noncoding transcript |
Het |
| Decr1 |
T |
A |
4: 15,924,261 (GRCm39) |
M220L |
probably benign |
Het |
| Dgkg |
T |
G |
16: 22,338,311 (GRCm39) |
D592A |
probably damaging |
Het |
| Dkkl1 |
T |
C |
7: 44,860,862 (GRCm39) |
Q39R |
probably benign |
Het |
| Dyrk1a |
T |
A |
16: 94,460,373 (GRCm39) |
C10S |
possibly damaging |
Het |
| Efcab2 |
A |
T |
1: 178,308,936 (GRCm39) |
E146D |
probably benign |
Het |
| Efhc1 |
T |
C |
1: 21,049,652 (GRCm39) |
V504A |
possibly damaging |
Het |
| Ermard |
T |
G |
17: 15,273,467 (GRCm39) |
|
probably null |
Het |
| Espl1 |
T |
C |
15: 102,224,247 (GRCm39) |
V1266A |
probably benign |
Het |
| Fbxw22 |
A |
C |
9: 109,232,465 (GRCm39) |
V40G |
probably damaging |
Het |
| Gm3629 |
A |
T |
14: 17,834,409 (GRCm39) |
I194N |
possibly damaging |
Het |
| Gnai2 |
C |
T |
9: 107,497,296 (GRCm39) |
V33M |
possibly damaging |
Het |
| H2-DMb1 |
T |
C |
17: 34,376,506 (GRCm39) |
|
probably null |
Het |
| Hc |
T |
C |
2: 34,879,851 (GRCm39) |
|
probably null |
Het |
| Iars1 |
T |
C |
13: 49,861,921 (GRCm39) |
S491P |
probably damaging |
Het |
| Knl1 |
T |
A |
2: 118,899,799 (GRCm39) |
L500H |
probably damaging |
Het |
| Lamb1 |
A |
T |
12: 31,319,146 (GRCm39) |
T102S |
probably damaging |
Het |
| Lrrc7 |
A |
G |
3: 157,866,373 (GRCm39) |
S1123P |
probably damaging |
Het |
| Mettl5 |
C |
A |
2: 69,702,071 (GRCm39) |
|
probably null |
Het |
| Mmp11 |
A |
G |
10: 75,759,818 (GRCm39) |
*4R |
probably null |
Het |
| Myom1 |
A |
T |
17: 71,389,483 (GRCm39) |
D911V |
probably benign |
Het |
| Nlrp4e |
G |
T |
7: 23,052,597 (GRCm39) |
V839L |
probably benign |
Het |
| Notch3 |
A |
T |
17: 32,370,128 (GRCm39) |
|
probably null |
Het |
| Or8k35 |
T |
C |
2: 86,424,411 (GRCm39) |
T254A |
possibly damaging |
Het |
| Pcdh8 |
T |
C |
14: 80,005,091 (GRCm39) |
H978R |
probably benign |
Het |
| Pde8b |
A |
T |
13: 95,178,508 (GRCm39) |
C537* |
probably null |
Het |
| Polr1b |
T |
C |
2: 128,967,366 (GRCm39) |
F920L |
probably damaging |
Het |
| Polr2f |
A |
G |
15: 79,035,573 (GRCm39) |
T87A |
probably damaging |
Het |
| Pon2 |
T |
A |
6: 5,272,421 (GRCm39) |
H133L |
probably damaging |
Het |
| Pou2af2 |
C |
T |
9: 51,201,481 (GRCm39) |
D192N |
probably damaging |
Het |
| Ptk2b |
T |
A |
14: 66,416,280 (GRCm39) |
E205V |
probably damaging |
Het |
| Rb1cc1 |
T |
A |
1: 6,314,357 (GRCm39) |
M343K |
probably benign |
Het |
| Rlf |
G |
A |
4: 121,005,807 (GRCm39) |
R1058W |
probably damaging |
Het |
| S100z |
T |
A |
13: 95,615,082 (GRCm39) |
K28* |
probably null |
Het |
| Scarf1 |
T |
A |
11: 75,411,141 (GRCm39) |
N273K |
probably benign |
Het |
| Setd2 |
A |
G |
9: 110,385,434 (GRCm39) |
I136M |
unknown |
Het |
| Sfrp2 |
A |
G |
3: 83,674,291 (GRCm39) |
D148G |
probably benign |
Het |
| Slc24a4 |
A |
G |
12: 102,220,769 (GRCm39) |
E400G |
probably benign |
Het |
| Slc2a9 |
T |
G |
5: 38,610,464 (GRCm39) |
I112L |
probably benign |
Het |
| Smc5 |
A |
T |
19: 23,186,312 (GRCm39) |
Y972* |
probably null |
Het |
| Sntg1 |
T |
C |
1: 8,515,248 (GRCm39) |
|
probably null |
Het |
| Spata31h1 |
T |
C |
10: 82,129,470 (GRCm39) |
N1180S |
probably benign |
Het |
| Stag1 |
A |
G |
9: 100,639,786 (GRCm39) |
D114G |
probably damaging |
Het |
| Suclg1 |
T |
C |
6: 73,233,192 (GRCm39) |
S46P |
probably damaging |
Het |
| Synj1 |
C |
T |
16: 90,743,703 (GRCm39) |
A1186T |
probably benign |
Het |
| Tas2r124 |
A |
G |
6: 132,732,410 (GRCm39) |
T240A |
probably benign |
Het |
| Tax1bp1 |
T |
C |
6: 52,721,341 (GRCm39) |
|
probably null |
Het |
| Tchh |
C |
A |
3: 93,355,158 (GRCm39) |
Q1533K |
unknown |
Het |
| Tmprss15 |
T |
C |
16: 78,759,058 (GRCm39) |
T887A |
probably benign |
Het |
| Ttn |
T |
C |
2: 76,536,937 (GRCm39) |
I34963V |
probably benign |
Het |
| Unc79 |
G |
A |
12: 103,078,878 (GRCm39) |
G1485D |
probably damaging |
Het |
| Usp9y |
G |
T |
Y: 1,385,355 (GRCm39) |
H633N |
probably benign |
Homo |
| Vmn2r99 |
A |
T |
17: 19,602,867 (GRCm39) |
N541Y |
probably damaging |
Het |
| Zbtb11 |
T |
A |
16: 55,810,854 (GRCm39) |
N337K |
probably benign |
Het |
| Zfp260 |
T |
A |
7: 29,804,267 (GRCm39) |
C56S |
possibly damaging |
Het |
| Zfp457 |
C |
T |
13: 67,440,746 (GRCm39) |
E610K |
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 |
|
|
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 |
|
|
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'- GAGGGAGAGATCACTTGCTG -3'
(R):5'- GCCACAGATTCCCAAGTGAC -3'
Sequencing Primer
(F):5'- ACAGTCTGTGTGATGAGACCC -3'
(R):5'- GTGACAACCACCACACTAGTG -3'
|
| Posted On |
2018-04-02 |
Incidental Mutation