Incidental Mutation 'R5427:Nid1'
ID |
426974 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Nid1
|
Ensembl Gene |
ENSMUSG00000005397 |
Gene Name |
nidogen 1 |
Synonyms |
nidogen-1, entactin, entactin 1, entactin-1 |
MMRRC Submission |
042993-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.227)
|
Stock # |
R5427 (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 13658268 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Cysteine
at position 671
(Y671C)
|
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: Y671C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000005532 Gene: ENSMUSG00000005397 AA Change: Y671C
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 |
0.4020 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
Validation Efficiency |
97% (58/60) |
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: 56 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aaas |
A |
G |
15: 102,248,385 (GRCm39) |
V277A |
possibly damaging |
Het |
Adcy7 |
G |
A |
8: 89,052,829 (GRCm39) |
|
probably null |
Het |
Adgrg5 |
A |
T |
8: 95,661,730 (GRCm39) |
D157V |
probably benign |
Het |
Akap13 |
A |
G |
7: 75,378,617 (GRCm39) |
N2090S |
possibly damaging |
Het |
Alpi |
T |
C |
1: 87,029,076 (GRCm39) |
N33D |
probably benign |
Het |
Anapc15 |
C |
T |
7: 101,547,810 (GRCm39) |
P68L |
probably damaging |
Het |
Ankrd34a |
G |
A |
3: 96,504,837 (GRCm39) |
G14R |
probably damaging |
Het |
Anp32a |
A |
G |
9: 62,284,598 (GRCm39) |
|
probably benign |
Het |
Atg4b |
G |
C |
1: 93,702,928 (GRCm39) |
K86N |
probably damaging |
Het |
Bbx |
T |
C |
16: 50,100,860 (GRCm39) |
T12A |
probably benign |
Het |
Catsperg2 |
T |
C |
7: 29,414,275 (GRCm39) |
T377A |
possibly damaging |
Het |
Ccdc158 |
T |
C |
5: 92,796,821 (GRCm39) |
Q505R |
probably damaging |
Het |
Cep135 |
T |
A |
5: 76,786,049 (GRCm39) |
S1051T |
probably benign |
Het |
Cryab |
A |
G |
9: 50,667,593 (GRCm39) |
D109G |
probably damaging |
Het |
Crym |
A |
C |
7: 119,798,445 (GRCm39) |
|
probably benign |
Het |
Csf2rb2 |
T |
A |
15: 78,173,111 (GRCm39) |
S250C |
probably damaging |
Het |
Diaph1 |
A |
T |
18: 38,023,648 (GRCm39) |
V730E |
unknown |
Het |
Eci3 |
G |
T |
13: 35,143,931 (GRCm39) |
L65M |
possibly damaging |
Het |
Erg28 |
T |
C |
12: 85,866,341 (GRCm39) |
N46D |
probably damaging |
Het |
Fam89b |
A |
G |
19: 5,778,819 (GRCm39) |
S127P |
probably benign |
Het |
Fign |
A |
G |
2: 63,809,342 (GRCm39) |
Y643H |
probably damaging |
Het |
Galk2 |
T |
C |
2: 125,788,741 (GRCm39) |
V265A |
probably benign |
Het |
Gclm |
T |
C |
3: 122,059,976 (GRCm39) |
V252A |
probably damaging |
Het |
Git2 |
A |
G |
5: 114,868,389 (GRCm39) |
S584P |
possibly damaging |
Het |
Iqcf3 |
T |
C |
9: 106,421,059 (GRCm39) |
|
probably null |
Het |
Kcnk3 |
A |
G |
5: 30,779,639 (GRCm39) |
T230A |
possibly damaging |
Het |
Mettl25b |
T |
C |
3: 87,831,639 (GRCm39) |
|
probably benign |
Het |
Myh10 |
T |
C |
11: 68,693,757 (GRCm39) |
L1486P |
probably damaging |
Het |
Myom2 |
C |
A |
8: 15,163,764 (GRCm39) |
A1006E |
probably benign |
Het |
Myt1l |
G |
A |
12: 29,882,331 (GRCm39) |
G509R |
unknown |
Het |
Nampt |
A |
T |
12: 32,884,914 (GRCm39) |
H111L |
probably benign |
Het |
Npy5r |
G |
A |
8: 67,133,672 (GRCm39) |
R374C |
probably damaging |
Het |
Or10ag54 |
A |
T |
2: 87,099,858 (GRCm39) |
K244N |
probably benign |
Het |
Or5b123 |
A |
T |
19: 13,596,714 (GRCm39) |
S20C |
probably benign |
Het |
Palld |
C |
T |
8: 62,003,106 (GRCm39) |
C720Y |
probably benign |
Het |
Pcsk6 |
C |
T |
7: 65,683,647 (GRCm39) |
T606M |
probably benign |
Het |
Pfas |
T |
C |
11: 68,891,979 (GRCm39) |
I176M |
possibly damaging |
Het |
Pi4kb |
A |
G |
3: 94,901,518 (GRCm39) |
D395G |
probably benign |
Het |
Plod3 |
A |
T |
5: 137,020,642 (GRCm39) |
Y547F |
probably damaging |
Het |
Plscr1l1 |
G |
A |
9: 92,234,649 (GRCm39) |
C128Y |
probably benign |
Het |
Pnpo |
T |
C |
11: 96,834,633 (GRCm39) |
Y21C |
probably benign |
Het |
Rgs1 |
A |
T |
1: 144,122,018 (GRCm39) |
C118* |
probably null |
Het |
Slc22a27 |
A |
G |
19: 7,856,753 (GRCm39) |
|
probably null |
Het |
Sntb1 |
C |
G |
15: 55,506,191 (GRCm39) |
G461R |
probably damaging |
Het |
Sppl2c |
G |
A |
11: 104,078,693 (GRCm39) |
V498I |
probably benign |
Het |
Stim2 |
A |
T |
5: 54,268,281 (GRCm39) |
I448F |
possibly damaging |
Het |
Sulf1 |
A |
T |
1: 12,867,136 (GRCm39) |
T107S |
possibly damaging |
Het |
Tenm3 |
A |
G |
8: 48,689,599 (GRCm39) |
V1996A |
probably damaging |
Het |
Timm23 |
G |
A |
14: 31,911,103 (GRCm39) |
T171I |
possibly damaging |
Het |
Tssk2 |
A |
G |
16: 17,716,729 (GRCm39) |
D44G |
probably damaging |
Het |
Vmn2r28 |
A |
T |
7: 5,489,376 (GRCm39) |
Y488N |
probably damaging |
Het |
Zbed6 |
A |
G |
1: 133,585,333 (GRCm39) |
V668A |
possibly damaging |
Het |
Zbtb48 |
A |
G |
4: 152,105,108 (GRCm39) |
F518S |
probably damaging |
Het |
Zfp709 |
A |
G |
8: 72,642,976 (GRCm39) |
E135G |
probably benign |
Het |
Zfp788 |
G |
A |
7: 41,299,076 (GRCm39) |
V571I |
possibly damaging |
Het |
Zfp963 |
A |
G |
8: 70,196,106 (GRCm39) |
S116P |
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 |
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 |
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'- AAGGGTATAGCTTGGTGGTCCC -3'
(R):5'- ACACTCAGCACATTCATTCTTG -3'
Sequencing Primer
(F):5'- GGTGGTCCCATTGTAGTACAACAC -3'
(R):5'- GTTTACAGAACCTGGAGGCTTCC -3'
|
Posted On |
2016-09-01 |