Incidental Mutation 'R2057:Nid1'
| ID |
228288 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nid1
|
| Ensembl Gene |
ENSMUSG00000005397 |
| Gene Name |
nidogen 1 |
| Synonyms |
nidogen-1, entactin, entactin 1, entactin-1 |
| MMRRC Submission |
040062-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.227)
|
| Stock # |
R2057 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
13612252-13686849 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 13675058 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Proline
at position 926
(H926P)
|
| 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: H926P
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: H926P
| 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 |
0.0627 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| 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: 78 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc2 |
A |
G |
19: 43,806,477 (GRCm39) |
K764E |
probably damaging |
Het |
| Abcg2 |
T |
C |
6: 58,667,525 (GRCm39) |
V129A |
probably benign |
Het |
| Adgrf5 |
A |
G |
17: 43,739,477 (GRCm39) |
Y72C |
possibly damaging |
Het |
| Ago1 |
C |
T |
4: 126,337,021 (GRCm39) |
R228H |
probably damaging |
Het |
| Ano1 |
A |
G |
7: 144,201,789 (GRCm39) |
V334A |
probably damaging |
Het |
| Apob |
A |
T |
12: 8,052,164 (GRCm39) |
R1202* |
probably null |
Het |
| Arfgap3 |
G |
T |
15: 83,194,501 (GRCm39) |
D389E |
probably benign |
Het |
| Atf6b |
A |
T |
17: 34,867,549 (GRCm39) |
|
probably null |
Het |
| Atoh8 |
T |
C |
6: 72,212,112 (GRCm39) |
K13E |
probably damaging |
Het |
| Bicral |
G |
T |
17: 47,135,814 (GRCm39) |
N465K |
possibly damaging |
Het |
| Bves |
T |
A |
10: 45,219,231 (GRCm39) |
Y110N |
probably damaging |
Het |
| C4b |
A |
G |
17: 34,947,594 (GRCm39) |
Y1695H |
probably damaging |
Het |
| Cage1 |
A |
G |
13: 38,207,356 (GRCm39) |
V163A |
probably benign |
Het |
| Canx |
T |
C |
11: 50,195,252 (GRCm39) |
N272S |
probably damaging |
Het |
| Caskin1 |
G |
T |
17: 24,715,433 (GRCm39) |
G93V |
probably damaging |
Het |
| Cd34 |
T |
C |
1: 194,641,450 (GRCm39) |
V292A |
probably damaging |
Het |
| Cd84 |
A |
G |
1: 171,700,317 (GRCm39) |
T145A |
possibly damaging |
Het |
| Cdh16 |
C |
A |
8: 105,348,597 (GRCm39) |
G144* |
probably null |
Het |
| Chaf1b |
T |
A |
16: 93,691,795 (GRCm39) |
H280Q |
probably damaging |
Het |
| Chpf2 |
G |
A |
5: 24,796,220 (GRCm39) |
G389R |
probably damaging |
Het |
| Crb1 |
T |
C |
1: 139,242,488 (GRCm39) |
Y330C |
probably damaging |
Het |
| Cux2 |
A |
T |
5: 122,007,567 (GRCm39) |
V698E |
probably benign |
Het |
| Dhtkd1 |
A |
G |
2: 5,947,430 (GRCm39) |
V18A |
unknown |
Het |
| Dmbt1 |
G |
A |
7: 130,707,900 (GRCm39) |
A1381T |
possibly damaging |
Het |
| Enpp1 |
C |
G |
10: 24,536,090 (GRCm39) |
A437P |
probably damaging |
Het |
| Fat2 |
C |
T |
11: 55,172,686 (GRCm39) |
V2676I |
possibly damaging |
Het |
| Fzd2 |
A |
G |
11: 102,496,759 (GRCm39) |
D401G |
probably damaging |
Het |
| Gcm2 |
T |
C |
13: 41,263,430 (GRCm39) |
M1V |
probably null |
Het |
| Gnai3 |
C |
T |
3: 108,019,812 (GRCm39) |
V233I |
probably benign |
Het |
| Golim4 |
T |
A |
3: 75,802,194 (GRCm39) |
D366V |
possibly damaging |
Het |
| Grin1 |
T |
A |
2: 25,206,832 (GRCm39) |
T110S |
probably damaging |
Het |
| Grin2a |
A |
G |
16: 9,487,608 (GRCm39) |
V430A |
probably benign |
Het |
| Gstp3 |
G |
A |
19: 4,109,282 (GRCm39) |
T5I |
probably damaging |
Het |
| Il17rb |
T |
A |
14: 29,719,111 (GRCm39) |
M324L |
probably benign |
Het |
| Jmy |
A |
G |
13: 93,596,211 (GRCm39) |
Y473H |
probably damaging |
Het |
| Khdc1b |
A |
G |
1: 21,454,534 (GRCm39) |
D79G |
probably benign |
Het |
| Kremen2 |
T |
C |
17: 23,961,691 (GRCm39) |
E272G |
possibly damaging |
Het |
| Lmo7 |
G |
C |
14: 102,124,614 (GRCm39) |
A358P |
probably damaging |
Het |
| Mdh1b |
T |
C |
1: 63,760,741 (GRCm39) |
I107V |
probably benign |
Het |
| Mlkl |
T |
C |
8: 112,060,242 (GRCm39) |
Q48R |
probably benign |
Het |
| Myh2 |
G |
A |
11: 67,079,665 (GRCm39) |
|
probably null |
Het |
| Naip1 |
T |
A |
13: 100,562,081 (GRCm39) |
Q1028L |
probably damaging |
Het |
| Ncald |
T |
A |
15: 37,397,423 (GRCm39) |
I86F |
possibly damaging |
Het |
| Nlrp9a |
T |
A |
7: 26,256,787 (GRCm39) |
I46K |
possibly damaging |
Het |
| Or1p1 |
A |
G |
11: 74,179,652 (GRCm39) |
Y60C |
probably damaging |
Het |
| Or9r3 |
A |
T |
10: 129,947,859 (GRCm39) |
S267T |
probably benign |
Het |
| Pak1 |
T |
A |
7: 97,557,004 (GRCm39) |
|
probably null |
Het |
| Parpbp |
T |
A |
10: 87,960,824 (GRCm39) |
M221L |
probably benign |
Het |
| Pde12 |
T |
C |
14: 26,390,035 (GRCm39) |
I225V |
probably benign |
Het |
| Phf19 |
G |
T |
2: 34,789,620 (GRCm39) |
R367S |
probably benign |
Het |
| Plcl2 |
A |
G |
17: 50,975,139 (GRCm39) |
|
probably null |
Het |
| Plxnb1 |
A |
T |
9: 108,938,294 (GRCm39) |
I1283F |
possibly damaging |
Het |
| Pramel6 |
T |
A |
2: 87,339,059 (GRCm39) |
N86K |
possibly damaging |
Het |
| Prkdc |
A |
G |
16: 15,545,469 (GRCm39) |
T1862A |
probably benign |
Het |
| Prpf40a |
A |
T |
2: 53,034,851 (GRCm39) |
I779K |
probably damaging |
Het |
| Prss3b |
G |
A |
6: 41,009,315 (GRCm39) |
T173I |
probably benign |
Het |
| Ptpn20 |
A |
T |
14: 33,352,942 (GRCm39) |
E227V |
probably damaging |
Het |
| Rad54b |
C |
T |
4: 11,606,088 (GRCm39) |
R499C |
probably benign |
Het |
| Rarg |
C |
A |
15: 102,147,939 (GRCm39) |
A291S |
probably damaging |
Het |
| Rnf169 |
A |
T |
7: 99,574,615 (GRCm39) |
L660Q |
probably damaging |
Het |
| Scn4a |
A |
G |
11: 106,226,550 (GRCm39) |
V670A |
probably damaging |
Het |
| Serpinb9c |
A |
T |
13: 33,340,854 (GRCm39) |
C81* |
probably null |
Het |
| Sik1 |
A |
G |
17: 32,067,771 (GRCm39) |
S435P |
probably benign |
Het |
| Slc35g2 |
G |
A |
9: 100,435,329 (GRCm39) |
A114V |
probably damaging |
Het |
| Slc7a14 |
A |
T |
3: 31,291,645 (GRCm39) |
V211E |
probably damaging |
Het |
| Snrpn |
A |
T |
7: 59,637,204 (GRCm39) |
H37Q |
possibly damaging |
Het |
| Spock3 |
T |
A |
8: 63,698,204 (GRCm39) |
C185* |
probably null |
Het |
| Tbc1d4 |
A |
G |
14: 101,714,591 (GRCm39) |
S627P |
probably damaging |
Het |
| Tgoln1 |
T |
C |
6: 72,592,653 (GRCm39) |
T276A |
probably benign |
Het |
| Tmem176b |
G |
A |
6: 48,813,267 (GRCm39) |
T64I |
probably damaging |
Het |
| Tnpo2 |
T |
C |
8: 85,776,742 (GRCm39) |
L483P |
probably damaging |
Het |
| Tpte |
T |
A |
8: 22,808,355 (GRCm39) |
D163E |
probably benign |
Het |
| Trim36 |
A |
T |
18: 46,329,229 (GRCm39) |
D70E |
probably benign |
Het |
| Umodl1 |
G |
A |
17: 31,227,740 (GRCm39) |
|
probably null |
Het |
| Wdr90 |
T |
C |
17: 26,074,173 (GRCm39) |
T691A |
probably benign |
Het |
| Zdhhc8 |
A |
G |
16: 18,046,210 (GRCm39) |
S118P |
probably damaging |
Het |
| Zfp438 |
T |
C |
18: 5,214,085 (GRCm39) |
E291G |
probably benign |
Het |
| Zfp879 |
C |
T |
11: 50,723,428 (GRCm39) |
E543K |
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 |
|
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'- ATATGTAGATGGGTGCATGAGC -3'
(R):5'- TTGGTAGCCAGGCCCCTATTAC -3'
Sequencing Primer
(F):5'- GCATGAGCACATATACACATATCTTC -3'
(R):5'- CTATTACTGGGACTGTCACCAGAG -3'
|
| Posted On |
2014-09-17 |
Incidental Mutation