Incidental Mutation 'R3409:Nod1'
| ID |
258417 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nod1
|
| Ensembl Gene |
ENSMUSG00000038058 |
| Gene Name |
nucleotide-binding oligomerization domain containing 1 |
| Synonyms |
Card4, F830007N14Rik, Nlrc1 |
| MMRRC Submission |
040627-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3409 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
54900934-54949597 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 54921902 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Serine
at position 139
(R139S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000130487
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000060655]
[ENSMUST00000168172]
[ENSMUST00000203076]
[ENSMUST00000203837]
|
| AlphaFold |
Q8BHB0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000060655
AA Change: R139S
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000055747
Gene: ENSMUSG00000038058
AA Change: R139S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
11 |
N/A |
INTRINSIC |
|
Pfam:CARD
|
20 |
105 |
4.7e-21 |
PFAM |
|
low complexity region
|
174 |
185 |
N/A |
INTRINSIC |
|
Pfam:NACHT
|
196 |
368 |
1.3e-41 |
PFAM |
|
low complexity region
|
515 |
529 |
N/A |
INTRINSIC |
|
low complexity region
|
555 |
565 |
N/A |
INTRINSIC |
|
low complexity region
|
708 |
717 |
N/A |
INTRINSIC |
|
LRR
|
727 |
754 |
1.25e0 |
SMART |
|
LRR
|
755 |
782 |
1.22e1 |
SMART |
|
LRR
|
783 |
810 |
1.96e2 |
SMART |
|
LRR
|
811 |
838 |
1.08e-1 |
SMART |
|
LRR
|
839 |
866 |
3.95e-4 |
SMART |
|
LRR
|
867 |
894 |
1.51e0 |
SMART |
|
LRR
|
895 |
922 |
7.15e-2 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000168172
AA Change: R139S
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000130487
Gene: ENSMUSG00000038058
AA Change: R139S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
11 |
N/A |
INTRINSIC |
|
Pfam:CARD
|
20 |
105 |
7.6e-20 |
PFAM |
|
low complexity region
|
174 |
185 |
N/A |
INTRINSIC |
|
Pfam:NACHT
|
196 |
368 |
6.2e-41 |
PFAM |
|
low complexity region
|
515 |
529 |
N/A |
INTRINSIC |
|
low complexity region
|
555 |
565 |
N/A |
INTRINSIC |
|
low complexity region
|
708 |
717 |
N/A |
INTRINSIC |
|
LRR
|
727 |
754 |
1.25e0 |
SMART |
|
LRR
|
755 |
782 |
1.22e1 |
SMART |
|
LRR
|
783 |
810 |
1.96e2 |
SMART |
|
LRR
|
811 |
838 |
1.08e-1 |
SMART |
|
LRR
|
839 |
866 |
3.95e-4 |
SMART |
|
LRR
|
867 |
894 |
1.51e0 |
SMART |
|
LRR
|
895 |
922 |
7.15e-2 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203076
|
| SMART Domains |
Protein: ENSMUSP00000145123
Gene: ENSMUSG00000038058
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
82 |
91 |
N/A |
INTRINSIC |
|
LRR
|
101 |
128 |
5.3e-3 |
SMART |
|
LRR
|
157 |
184 |
4.8e-4 |
SMART |
|
LRR
|
185 |
212 |
1.7e-6 |
SMART |
|
LRR
|
213 |
240 |
6.4e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000203837
|
| SMART Domains |
Protein: ENSMUSP00000145005
Gene: ENSMUSG00000038058
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
11 |
N/A |
INTRINSIC |
|
PDB:2NZ7|B
|
13 |
52 |
4e-14 |
PDB |
|
Blast:CARD
|
17 |
52 |
1e-14 |
BLAST |
|
| Meta Mutation Damage Score |
0.1000 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 91.4%
|
| 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 NOD (nucleotide-binding oligomerization domain) family. This member is a cytosolic protein. It contains an N-terminal caspase recruitment domain (CARD), a centrally located nucleotide-binding domain (NBD), and 10 tandem leucine-rich repeats (LRRs) in its C terminus. The CARD is involved in apoptotic signaling, LRRs participate in protein-protein interactions, and mutations in the NBD may affect the process of oligomerization and subsequent function of the LRR domain. This protein is an intracellular pattern-recognition receptor (PRR) that initiates inflammation in response to a subset of bacteria through the detection of bacterial diaminopimelic acid. Multiple alternatively spliced transcript variants differring in the 5' UTR have been described, but the full-length nature of these variants has not been determined. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous mutant mice were viable, fertile, and appeared normal in a specific-pathogen free environment. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgra3 |
A |
G |
5: 50,159,272 (GRCm39) |
V326A |
probably damaging |
Het |
| AI429214 |
C |
T |
8: 37,461,071 (GRCm39) |
S73L |
probably benign |
Het |
| Atp13a4 |
G |
T |
16: 29,232,567 (GRCm39) |
T923K |
probably damaging |
Het |
| Ccdc150 |
A |
G |
1: 54,395,932 (GRCm39) |
D805G |
probably benign |
Het |
| Ccdc185 |
T |
G |
1: 182,576,313 (GRCm39) |
Q125H |
possibly damaging |
Het |
| Ccdc88a |
T |
A |
11: 29,436,006 (GRCm39) |
C10S |
probably damaging |
Het |
| Cpsf1 |
G |
T |
15: 76,485,981 (GRCm39) |
Y396* |
probably null |
Het |
| Dnpep |
A |
G |
1: 75,293,270 (GRCm39) |
V33A |
probably damaging |
Het |
| Fbn1 |
G |
A |
2: 125,254,585 (GRCm39) |
A226V |
possibly damaging |
Het |
| Frmd4a |
A |
T |
2: 4,157,839 (GRCm39) |
|
probably benign |
Het |
| Gipr |
A |
G |
7: 18,893,719 (GRCm39) |
V318A |
possibly damaging |
Het |
| Gsdmc4 |
A |
G |
15: 63,763,895 (GRCm39) |
S401P |
probably benign |
Het |
| H2-M10.6 |
T |
A |
17: 37,124,893 (GRCm39) |
V270E |
probably damaging |
Het |
| Klhl7 |
G |
T |
5: 24,343,319 (GRCm39) |
V212L |
probably damaging |
Het |
| Krt10 |
C |
A |
11: 99,278,087 (GRCm39) |
R322L |
probably damaging |
Het |
| Lrrn4 |
A |
G |
2: 132,721,781 (GRCm39) |
L12P |
unknown |
Het |
| Mast2 |
C |
G |
4: 116,168,107 (GRCm39) |
E881Q |
possibly damaging |
Het |
| Notch3 |
C |
T |
17: 32,369,676 (GRCm39) |
V772M |
possibly damaging |
Het |
| Nrxn1 |
G |
A |
17: 90,515,795 (GRCm39) |
T19M |
probably damaging |
Het |
| Nudcd1 |
T |
C |
15: 44,284,207 (GRCm39) |
M60V |
probably benign |
Het |
| Or10g1 |
T |
A |
14: 52,647,818 (GRCm39) |
R170S |
possibly damaging |
Het |
| Or4c1 |
A |
G |
2: 89,133,717 (GRCm39) |
F73S |
probably benign |
Het |
| Or4c115 |
T |
C |
2: 88,927,668 (GRCm39) |
N201S |
possibly damaging |
Het |
| Or5b101 |
G |
C |
19: 13,005,411 (GRCm39) |
A94G |
probably benign |
Het |
| Or5w8 |
T |
A |
2: 87,688,005 (GRCm39) |
L162* |
probably null |
Het |
| Or8c9 |
T |
A |
9: 38,241,640 (GRCm39) |
S252R |
possibly damaging |
Het |
| Pcdhb6 |
A |
G |
18: 37,468,945 (GRCm39) |
E622G |
probably damaging |
Het |
| Pitrm1 |
G |
A |
13: 6,628,517 (GRCm39) |
A937T |
possibly damaging |
Het |
| Plxnb1 |
G |
A |
9: 108,935,681 (GRCm39) |
|
probably null |
Het |
| Ripk3 |
T |
G |
14: 56,025,698 (GRCm39) |
N54T |
probably damaging |
Het |
| Rpn2 |
C |
A |
2: 157,132,572 (GRCm39) |
A108E |
possibly damaging |
Het |
| Scaf11 |
A |
G |
15: 96,312,745 (GRCm39) |
V1432A |
probably damaging |
Het |
| Sec14l5 |
C |
T |
16: 4,983,518 (GRCm39) |
|
probably null |
Het |
| Serpina3n |
A |
G |
12: 104,377,536 (GRCm39) |
E263G |
possibly damaging |
Het |
| Six4 |
A |
G |
12: 73,159,657 (GRCm39) |
F101S |
probably damaging |
Het |
| Slc12a1 |
A |
G |
2: 124,996,071 (GRCm39) |
T75A |
probably benign |
Het |
| Slc26a9 |
T |
C |
1: 131,691,682 (GRCm39) |
S642P |
probably benign |
Het |
| Smu1 |
T |
C |
4: 40,752,008 (GRCm39) |
T183A |
probably benign |
Het |
| Sptb |
T |
G |
12: 76,657,589 (GRCm39) |
K1311Q |
possibly damaging |
Het |
| Tal2 |
A |
G |
4: 53,785,843 (GRCm39) |
N8S |
probably damaging |
Het |
| Tenm4 |
A |
G |
7: 96,544,367 (GRCm39) |
T2128A |
probably damaging |
Het |
| Tmem67 |
A |
T |
4: 12,073,952 (GRCm39) |
M288K |
probably benign |
Het |
| Ubr1 |
A |
C |
2: 120,793,929 (GRCm39) |
I85S |
probably benign |
Het |
| Vmn2r90 |
G |
T |
17: 17,953,638 (GRCm39) |
V601L |
probably benign |
Het |
| Zfhx4 |
C |
T |
3: 5,468,418 (GRCm39) |
P2859S |
probably benign |
Het |
|
| Other mutations in Nod1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00822:Nod1
|
APN |
6 |
54,921,931 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00937:Nod1
|
APN |
6 |
54,914,349 (GRCm39) |
missense |
probably benign |
0.08 |
|
IGL00945:Nod1
|
APN |
6 |
54,921,571 (GRCm39) |
splice site |
probably null |
|
|
IGL01410:Nod1
|
APN |
6 |
54,921,341 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02094:Nod1
|
APN |
6 |
54,916,375 (GRCm39) |
splice site |
probably null |
|
|
IGL02217:Nod1
|
APN |
6 |
54,920,404 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
IGL02573:Nod1
|
APN |
6 |
54,920,930 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL02944:Nod1
|
APN |
6 |
54,901,932 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R0092:Nod1
|
UTSW |
6 |
54,921,526 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0108:Nod1
|
UTSW |
6 |
54,920,734 (GRCm39) |
missense |
probably benign |
0.27 |
|
R0148:Nod1
|
UTSW |
6 |
54,915,202 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0771:Nod1
|
UTSW |
6 |
54,921,254 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1493:Nod1
|
UTSW |
6 |
54,921,041 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1540:Nod1
|
UTSW |
6 |
54,920,960 (GRCm39) |
missense |
probably benign |
0.09 |
|
R1660:Nod1
|
UTSW |
6 |
54,921,218 (GRCm39) |
splice site |
probably null |
|
|
R1710:Nod1
|
UTSW |
6 |
54,921,044 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1911:Nod1
|
UTSW |
6 |
54,921,425 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R2008:Nod1
|
UTSW |
6 |
54,916,310 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3410:Nod1
|
UTSW |
6 |
54,921,902 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3927:Nod1
|
UTSW |
6 |
54,921,902 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4499:Nod1
|
UTSW |
6 |
54,920,981 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4608:Nod1
|
UTSW |
6 |
54,920,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5552:Nod1
|
UTSW |
6 |
54,921,616 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5667:Nod1
|
UTSW |
6 |
54,910,561 (GRCm39) |
missense |
probably benign |
0.06 |
|
R5859:Nod1
|
UTSW |
6 |
54,907,162 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5868:Nod1
|
UTSW |
6 |
54,916,312 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5995:Nod1
|
UTSW |
6 |
54,921,539 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6329:Nod1
|
UTSW |
6 |
54,921,689 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6331:Nod1
|
UTSW |
6 |
54,901,968 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6642:Nod1
|
UTSW |
6 |
54,925,014 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6798:Nod1
|
UTSW |
6 |
54,921,596 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6889:Nod1
|
UTSW |
6 |
54,921,094 (GRCm39) |
missense |
probably benign |
0.27 |
|
R7582:Nod1
|
UTSW |
6 |
54,921,292 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8123:Nod1
|
UTSW |
6 |
54,914,391 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8317:Nod1
|
UTSW |
6 |
54,920,425 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8338:Nod1
|
UTSW |
6 |
54,920,956 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8524:Nod1
|
UTSW |
6 |
54,925,060 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8896:Nod1
|
UTSW |
6 |
54,921,277 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8961:Nod1
|
UTSW |
6 |
54,926,461 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CGAACACGAAGACAGTCTCG -3'
(R):5'- TCTGGGACACTGGCTCTTTG -3'
Sequencing Primer
(F):5'- GAAGACAGTCTCGCCATGCTC -3'
(R):5'- CTCCTGTTAGAGTAATTGATCTGGC -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation