Incidental Mutation 'R0384:Nid1'
| ID |
31191 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nid1
|
| Ensembl Gene |
ENSMUSG00000005397 |
| Gene Name |
nidogen 1 |
| Synonyms |
nidogen-1, entactin, entactin 1, entactin-1 |
| MMRRC Submission |
038590-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.227)
|
| Stock # |
R0384 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
13612252-13686849 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 13638421 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 114
(T114A)
|
| 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: T114A
PolyPhen 2
Score 0.345 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: T114A
| 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 |
0.2770 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 91.7%
|
| Validation Efficiency |
100% (72/72) |
| 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 |
|---|
| Adam8 |
T |
A |
7: 139,566,725 (GRCm39) |
|
probably benign |
Het |
| Akr1b8 |
T |
C |
6: 34,341,265 (GRCm39) |
|
probably benign |
Het |
| Arhgef39 |
A |
G |
4: 43,498,613 (GRCm39) |
L117P |
probably damaging |
Het |
| Atp13a1 |
A |
T |
8: 70,249,974 (GRCm39) |
Q356L |
possibly damaging |
Het |
| Bmp2k |
T |
A |
5: 97,178,984 (GRCm39) |
|
probably benign |
Het |
| Ccdc141 |
A |
G |
2: 76,857,992 (GRCm39) |
V1063A |
probably damaging |
Het |
| Col20a1 |
T |
C |
2: 180,640,955 (GRCm39) |
Y568H |
probably benign |
Het |
| Crabp2 |
T |
C |
3: 87,860,328 (GRCm39) |
V134A |
possibly damaging |
Het |
| Cyp19a1 |
T |
C |
9: 54,080,025 (GRCm39) |
K265E |
probably benign |
Het |
| Cyp2j9 |
T |
C |
4: 96,474,122 (GRCm39) |
H106R |
probably benign |
Het |
| Dcps |
T |
C |
9: 35,087,239 (GRCm39) |
K9R |
probably damaging |
Het |
| Dnajc6 |
C |
T |
4: 101,456,153 (GRCm39) |
T47I |
probably damaging |
Het |
| Dnhd1 |
T |
G |
7: 105,369,321 (GRCm39) |
S4315A |
possibly damaging |
Het |
| Dnmt3l |
A |
T |
10: 77,888,571 (GRCm39) |
I158F |
possibly damaging |
Het |
| Dock3 |
A |
G |
9: 106,779,094 (GRCm39) |
|
probably benign |
Het |
| Eefsec |
A |
G |
6: 88,258,632 (GRCm39) |
|
probably null |
Het |
| Fam204a |
T |
C |
19: 60,209,728 (GRCm39) |
M1V |
probably null |
Het |
| Fam98b |
T |
C |
2: 117,098,328 (GRCm39) |
V266A |
possibly damaging |
Het |
| Fat2 |
A |
T |
11: 55,160,291 (GRCm39) |
I3274N |
possibly damaging |
Het |
| Fbh1 |
A |
G |
2: 11,754,389 (GRCm39) |
I198T |
probably damaging |
Het |
| Fer |
T |
C |
17: 64,231,179 (GRCm39) |
|
probably benign |
Het |
| Fhad1 |
T |
A |
4: 141,729,737 (GRCm39) |
M89L |
probably benign |
Het |
| Fjx1 |
C |
A |
2: 102,281,452 (GRCm39) |
C161F |
probably damaging |
Het |
| Fkbp7 |
T |
A |
2: 76,496,168 (GRCm39) |
|
probably benign |
Het |
| Gm42669 |
T |
A |
5: 107,656,664 (GRCm39) |
C976S |
probably benign |
Het |
| Gm4845 |
T |
C |
1: 141,184,823 (GRCm39) |
|
noncoding transcript |
Het |
| Herc1 |
T |
A |
9: 66,388,332 (GRCm39) |
|
probably benign |
Het |
| Hook3 |
C |
T |
8: 26,534,263 (GRCm39) |
|
probably null |
Het |
| Idh2 |
C |
T |
7: 79,748,005 (GRCm39) |
A232T |
probably damaging |
Het |
| Itga2b |
A |
T |
11: 102,356,188 (GRCm39) |
|
probably null |
Het |
| Klk1b21 |
T |
C |
7: 43,754,917 (GRCm39) |
Y71H |
probably benign |
Het |
| Kndc1 |
A |
T |
7: 139,490,515 (GRCm39) |
N339I |
possibly damaging |
Het |
| Ky |
C |
T |
9: 102,419,289 (GRCm39) |
T432I |
probably benign |
Het |
| Map4 |
C |
T |
9: 109,863,696 (GRCm39) |
T307I |
probably damaging |
Het |
| Matn1 |
T |
C |
4: 130,671,787 (GRCm39) |
L18P |
probably benign |
Het |
| Mindy4 |
G |
A |
6: 55,193,669 (GRCm39) |
D121N |
probably damaging |
Het |
| Mpv17l |
A |
T |
16: 13,758,863 (GRCm39) |
I96L |
probably benign |
Het |
| Msto1 |
G |
A |
3: 88,817,646 (GRCm39) |
Q441* |
probably null |
Het |
| Muc5ac |
A |
G |
7: 141,365,988 (GRCm39) |
H2048R |
possibly damaging |
Het |
| Musk |
T |
C |
4: 58,373,711 (GRCm39) |
*879Q |
probably null |
Het |
| Nat8f2 |
T |
C |
6: 85,845,350 (GRCm39) |
Y4C |
possibly damaging |
Het |
| Ncaph2 |
T |
A |
15: 89,253,594 (GRCm39) |
I282N |
probably benign |
Het |
| Npr1 |
C |
A |
3: 90,372,474 (GRCm39) |
G113C |
probably damaging |
Het |
| Nrxn1 |
G |
A |
17: 90,515,775 (GRCm39) |
P193S |
probably damaging |
Het |
| Nwd2 |
T |
C |
5: 63,963,025 (GRCm39) |
F870L |
probably benign |
Het |
| Or10h1b |
A |
G |
17: 33,395,522 (GRCm39) |
I45V |
probably damaging |
Het |
| Or4c122 |
A |
G |
2: 89,079,414 (GRCm39) |
I208T |
possibly damaging |
Het |
| Or6c5c |
T |
A |
10: 129,298,909 (GRCm39) |
Y121* |
probably null |
Het |
| Or8k30 |
T |
A |
2: 86,339,727 (GRCm39) |
I308K |
possibly damaging |
Het |
| Phf14 |
A |
G |
6: 11,997,019 (GRCm39) |
|
probably benign |
Het |
| Pnpla5 |
G |
T |
15: 84,004,920 (GRCm39) |
L144M |
probably damaging |
Het |
| Prdm2 |
T |
C |
4: 142,862,258 (GRCm39) |
E344G |
probably benign |
Het |
| Psmd12 |
T |
C |
11: 107,376,547 (GRCm39) |
V61A |
probably benign |
Het |
| Relt |
T |
C |
7: 100,496,712 (GRCm39) |
D385G |
probably benign |
Het |
| Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
| Scg2 |
T |
A |
1: 79,413,266 (GRCm39) |
I446F |
probably benign |
Het |
| Sema3b |
G |
A |
9: 107,478,165 (GRCm39) |
L407F |
probably damaging |
Het |
| Slc25a13 |
A |
T |
6: 6,042,600 (GRCm39) |
Y601* |
probably null |
Het |
| Sun5 |
C |
T |
2: 153,700,885 (GRCm39) |
V270I |
probably benign |
Het |
| Tex52 |
A |
G |
6: 128,356,496 (GRCm39) |
Y63C |
probably damaging |
Het |
| Tmem138 |
A |
G |
19: 10,552,186 (GRCm39) |
|
probably benign |
Het |
| Tnpo3 |
A |
G |
6: 29,582,163 (GRCm39) |
|
probably null |
Het |
| Tspoap1 |
A |
T |
11: 87,657,280 (GRCm39) |
Q364L |
probably damaging |
Het |
| Ttc41 |
T |
C |
10: 86,599,811 (GRCm39) |
L1037P |
probably damaging |
Het |
| Ugcg |
T |
A |
4: 59,220,387 (GRCm39) |
D393E |
possibly damaging |
Het |
| Vmn1r184 |
T |
C |
7: 25,967,076 (GRCm39) |
I274T |
probably benign |
Het |
| Vmn2r27 |
A |
G |
6: 124,200,871 (GRCm39) |
V362A |
probably benign |
Het |
| Vmn2r87 |
T |
A |
10: 130,307,712 (GRCm39) |
Y842F |
probably benign |
Het |
| Vps8 |
T |
A |
16: 21,325,575 (GRCm39) |
|
probably benign |
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 |
|
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 |
|
|
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'- CAACTGCAACAGTATCCGGTGAGG -3'
(R):5'- CATAAGGGGCCACAGATTCCCAAG -3'
Sequencing Primer
(F):5'- ttagagcacagagagcaagg -3'
(R):5'- ACAGATTCCCAAGTGACAACC -3'
|
| Posted On |
2013-04-24 |
Incidental Mutation