Incidental Mutation 'R1559:Lrrc4c'
| ID |
170475 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrrc4c
|
| Ensembl Gene |
ENSMUSG00000050587 |
| Gene Name |
leucine rich repeat containing 4C |
| Synonyms |
6430556C10Rik, netrin g1 ligand, NGL-1 |
| MMRRC Submission |
039598-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.081)
|
| Stock # |
R1559 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
96148514-97462011 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 97461117 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 581
(M581K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125218
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000059049]
[ENSMUST00000135431]
[ENSMUST00000162807]
[ENSMUST00000170144]
|
| AlphaFold |
Q8C031 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000059049
AA Change: M581K
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: M581K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
26 |
42 |
N/A |
INTRINSIC |
|
LRRNT
|
46 |
80 |
6.95e-4 |
SMART |
|
LRR
|
79 |
98 |
1.97e2 |
SMART |
|
LRR_TYP
|
99 |
122 |
7.37e-4 |
SMART |
|
LRR
|
123 |
146 |
1.08e-1 |
SMART |
|
LRR_TYP
|
147 |
170 |
1.38e-3 |
SMART |
|
Blast:LRR
|
171 |
195 |
5e-8 |
BLAST |
|
LRR
|
196 |
217 |
8.03e1 |
SMART |
|
LRR_TYP
|
218 |
241 |
2.12e-4 |
SMART |
|
LRR
|
242 |
265 |
6.97e1 |
SMART |
|
LRR_TYP
|
266 |
289 |
2.53e-2 |
SMART |
|
LRRCT
|
301 |
352 |
2.68e-2 |
SMART |
|
IGc2
|
366 |
433 |
1.22e-7 |
SMART |
|
transmembrane domain
|
526 |
548 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000135431
AA Change: M581K
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: M581K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
26 |
42 |
N/A |
INTRINSIC |
|
LRRNT
|
46 |
80 |
6.95e-4 |
SMART |
|
LRR
|
79 |
98 |
1.97e2 |
SMART |
|
LRR_TYP
|
99 |
122 |
7.37e-4 |
SMART |
|
LRR
|
123 |
146 |
1.08e-1 |
SMART |
|
LRR_TYP
|
147 |
170 |
1.38e-3 |
SMART |
|
Blast:LRR
|
171 |
195 |
5e-8 |
BLAST |
|
LRR
|
196 |
217 |
8.03e1 |
SMART |
|
LRR_TYP
|
218 |
241 |
2.12e-4 |
SMART |
|
LRR
|
242 |
265 |
6.97e1 |
SMART |
|
LRR_TYP
|
266 |
289 |
2.53e-2 |
SMART |
|
LRRCT
|
301 |
352 |
2.68e-2 |
SMART |
|
IGc2
|
366 |
433 |
1.22e-7 |
SMART |
|
transmembrane domain
|
526 |
548 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000162807
AA Change: M581K
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: M581K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
26 |
42 |
N/A |
INTRINSIC |
|
LRRNT
|
46 |
80 |
6.95e-4 |
SMART |
|
LRR
|
79 |
98 |
1.97e2 |
SMART |
|
LRR_TYP
|
99 |
122 |
7.37e-4 |
SMART |
|
LRR
|
123 |
146 |
1.08e-1 |
SMART |
|
LRR_TYP
|
147 |
170 |
1.38e-3 |
SMART |
|
Blast:LRR
|
171 |
195 |
5e-8 |
BLAST |
|
LRR
|
196 |
217 |
8.03e1 |
SMART |
|
LRR_TYP
|
218 |
241 |
2.12e-4 |
SMART |
|
LRR
|
242 |
265 |
6.97e1 |
SMART |
|
LRR_TYP
|
266 |
289 |
2.53e-2 |
SMART |
|
LRRCT
|
301 |
352 |
2.68e-2 |
SMART |
|
IGc2
|
366 |
433 |
1.22e-7 |
SMART |
|
transmembrane domain
|
526 |
548 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170144
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000199276
|
| Meta Mutation Damage Score |
0.0698 |
| Coding Region Coverage |
- 1x: 98.8%
- 3x: 97.7%
- 10x: 94.0%
- 20x: 84.8%
|
| Validation Efficiency |
95% (73/77) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygous mutant mice exhibited an increased mean serum IL-6 response to LPS challenge when compared with controls. No other notable phenotype was detected in a high-througput screen. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
T |
A |
11: 9,349,180 (GRCm39) |
W3585R |
probably null |
Het |
| Ajm1 |
G |
T |
2: 25,467,043 (GRCm39) |
S956* |
probably null |
Het |
| Babam1 |
G |
C |
8: 71,850,424 (GRCm39) |
E18Q |
probably damaging |
Het |
| Bcan |
G |
T |
3: 87,901,519 (GRCm39) |
S394R |
probably damaging |
Het |
| Birc6 |
T |
A |
17: 74,999,232 (GRCm39) |
F4653L |
probably damaging |
Het |
| Camsap2 |
A |
T |
1: 136,209,832 (GRCm39) |
H559Q |
probably benign |
Het |
| Cars2 |
G |
T |
8: 11,580,430 (GRCm39) |
|
probably null |
Het |
| Ccdc93 |
T |
A |
1: 121,389,712 (GRCm39) |
|
probably benign |
Het |
| Ccna2 |
C |
A |
3: 36,624,879 (GRCm39) |
|
probably benign |
Het |
| Cdc6 |
T |
A |
11: 98,803,037 (GRCm39) |
L326I |
probably damaging |
Het |
| Cdh23 |
A |
T |
10: 60,255,478 (GRCm39) |
|
probably benign |
Het |
| Cenpe |
T |
A |
3: 134,976,661 (GRCm39) |
S2423T |
probably benign |
Het |
| Cftr |
A |
G |
6: 18,225,936 (GRCm39) |
M295V |
probably benign |
Het |
| Cxcl2 |
A |
G |
5: 91,051,871 (GRCm39) |
H23R |
probably benign |
Het |
| Cyp4a12b |
A |
G |
4: 115,291,181 (GRCm39) |
T370A |
probably damaging |
Het |
| Daam2 |
A |
G |
17: 49,803,148 (GRCm39) |
|
probably benign |
Het |
| Dclk3 |
T |
C |
9: 111,298,276 (GRCm39) |
F607L |
probably damaging |
Het |
| Des |
T |
G |
1: 75,337,230 (GRCm39) |
S57A |
probably benign |
Het |
| Drd1 |
A |
T |
13: 54,206,964 (GRCm39) |
S410T |
probably damaging |
Het |
| Ecm1 |
G |
A |
3: 95,643,275 (GRCm39) |
R342C |
probably damaging |
Het |
| Fanci |
T |
C |
7: 79,082,941 (GRCm39) |
L639P |
probably damaging |
Het |
| Fancm |
A |
G |
12: 65,140,463 (GRCm39) |
E395G |
probably benign |
Het |
| Grik3 |
A |
G |
4: 125,601,790 (GRCm39) |
D889G |
probably benign |
Het |
| Heyl |
A |
G |
4: 123,135,192 (GRCm39) |
S62G |
probably damaging |
Het |
| Hmox1 |
C |
T |
8: 75,826,577 (GRCm39) |
P267L |
probably damaging |
Het |
| Ifi213 |
A |
C |
1: 173,394,784 (GRCm39) |
S584A |
probably benign |
Het |
| Il12rb2 |
G |
T |
6: 67,333,576 (GRCm39) |
F234L |
probably benign |
Het |
| Il4i1 |
T |
A |
7: 44,488,811 (GRCm39) |
S233T |
probably damaging |
Het |
| Itga4 |
A |
G |
2: 79,146,032 (GRCm39) |
S745G |
probably benign |
Het |
| Kalrn |
T |
A |
16: 33,830,918 (GRCm39) |
I734F |
possibly damaging |
Het |
| Klk1b16 |
T |
C |
7: 43,790,425 (GRCm39) |
I200T |
probably benign |
Het |
| M6pr |
A |
T |
6: 122,292,033 (GRCm39) |
I122L |
probably benign |
Het |
| Magi3 |
T |
C |
3: 103,954,169 (GRCm39) |
|
probably benign |
Het |
| Mybpc2 |
T |
G |
7: 44,163,111 (GRCm39) |
T480P |
probably benign |
Het |
| Or14c44 |
T |
C |
7: 86,061,575 (GRCm39) |
S43P |
probably benign |
Het |
| Or1j17 |
A |
G |
2: 36,578,770 (GRCm39) |
Y252C |
probably damaging |
Het |
| Or51ab3 |
A |
T |
7: 103,201,372 (GRCm39) |
I127F |
possibly damaging |
Het |
| Or8g23 |
T |
C |
9: 38,971,437 (GRCm39) |
N175S |
probably benign |
Het |
| Pcx |
T |
A |
19: 4,669,114 (GRCm39) |
I704N |
probably damaging |
Het |
| Pde3a |
G |
T |
6: 141,404,824 (GRCm39) |
A350S |
probably damaging |
Het |
| Ppox |
A |
T |
1: 171,107,580 (GRCm39) |
|
probably benign |
Het |
| Prb1a |
T |
A |
6: 132,185,507 (GRCm39) |
Y42F |
unknown |
Het |
| Rsph4a |
T |
A |
10: 33,785,727 (GRCm39) |
V546E |
probably damaging |
Het |
| Saxo4 |
T |
C |
19: 10,458,770 (GRCm39) |
T87A |
probably benign |
Het |
| Sf3b1 |
C |
G |
1: 55,058,554 (GRCm39) |
E12Q |
possibly damaging |
Het |
| Sh3tc1 |
A |
G |
5: 35,860,693 (GRCm39) |
|
probably null |
Het |
| Slc22a2 |
T |
C |
17: 12,803,298 (GRCm39) |
F44S |
probably damaging |
Het |
| Slco6c1 |
T |
A |
1: 97,026,223 (GRCm39) |
D334V |
probably damaging |
Het |
| Smim19 |
T |
C |
8: 22,953,352 (GRCm39) |
D105G |
probably damaging |
Het |
| Smpdl3a |
A |
G |
10: 57,683,588 (GRCm39) |
T233A |
probably damaging |
Het |
| St8sia5 |
G |
A |
18: 77,299,460 (GRCm39) |
|
probably null |
Het |
| Stk32a |
C |
A |
18: 43,376,149 (GRCm39) |
Q73K |
probably benign |
Het |
| Tmem129 |
G |
T |
5: 33,815,100 (GRCm39) |
|
probably null |
Het |
| Traf3ip3 |
A |
T |
1: 192,860,599 (GRCm39) |
L441Q |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,731,305 (GRCm39) |
|
probably benign |
Het |
| Unc45b |
T |
C |
11: 82,808,672 (GRCm39) |
S253P |
possibly damaging |
Het |
| Vars2 |
A |
G |
17: 35,977,150 (GRCm39) |
|
probably benign |
Het |
| Vmn2r51 |
C |
T |
7: 9,836,372 (GRCm39) |
M136I |
possibly damaging |
Het |
| Vmn2r51 |
A |
G |
7: 9,836,373 (GRCm39) |
M136T |
possibly damaging |
Het |
| Zfp595 |
T |
C |
13: 67,465,127 (GRCm39) |
I379V |
possibly damaging |
Het |
|
| Other mutations in Lrrc4c |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00482:Lrrc4c
|
APN |
2 |
97,460,730 (GRCm39) |
nonsense |
probably null |
|
|
IGL02095:Lrrc4c
|
APN |
2 |
97,459,749 (GRCm39) |
missense |
probably benign |
0.05 |
|
IGL02165:Lrrc4c
|
APN |
2 |
97,459,378 (GRCm39) |
start codon destroyed |
probably null |
0.33 |
|
IGL02176:Lrrc4c
|
APN |
2 |
97,460,598 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL02674:Lrrc4c
|
APN |
2 |
97,460,120 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03082:Lrrc4c
|
APN |
2 |
97,460,931 (GRCm39) |
missense |
probably benign |
0.05 |
|
IGL03303:Lrrc4c
|
APN |
2 |
97,459,937 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0946:Lrrc4c
|
UTSW |
2 |
97,459,809 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1037:Lrrc4c
|
UTSW |
2 |
97,460,330 (GRCm39) |
missense |
probably benign |
|
|
R1518:Lrrc4c
|
UTSW |
2 |
97,460,921 (GRCm39) |
missense |
probably benign |
|
|
R2192:Lrrc4c
|
UTSW |
2 |
97,459,657 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R2213:Lrrc4c
|
UTSW |
2 |
97,460,816 (GRCm39) |
missense |
probably benign |
0.29 |
|
R2279:Lrrc4c
|
UTSW |
2 |
97,460,850 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R3552:Lrrc4c
|
UTSW |
2 |
97,460,306 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3840:Lrrc4c
|
UTSW |
2 |
97,460,537 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3841:Lrrc4c
|
UTSW |
2 |
97,460,537 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4606:Lrrc4c
|
UTSW |
2 |
97,460,658 (GRCm39) |
missense |
probably benign |
0.22 |
|
R4938:Lrrc4c
|
UTSW |
2 |
97,459,646 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4946:Lrrc4c
|
UTSW |
2 |
97,460,834 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5323:Lrrc4c
|
UTSW |
2 |
97,460,498 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6014:Lrrc4c
|
UTSW |
2 |
97,459,557 (GRCm39) |
splice site |
probably null |
|
|
R6297:Lrrc4c
|
UTSW |
2 |
97,459,964 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6376:Lrrc4c
|
UTSW |
2 |
97,459,391 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7032:Lrrc4c
|
UTSW |
2 |
97,459,410 (GRCm39) |
missense |
probably benign |
|
|
R7419:Lrrc4c
|
UTSW |
2 |
97,460,106 (GRCm39) |
missense |
probably benign |
0.07 |
|
R7699:Lrrc4c
|
UTSW |
2 |
97,461,024 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R7700:Lrrc4c
|
UTSW |
2 |
97,461,024 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R7723:Lrrc4c
|
UTSW |
2 |
97,460,999 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7736:Lrrc4c
|
UTSW |
2 |
97,460,705 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7843:Lrrc4c
|
UTSW |
2 |
97,460,558 (GRCm39) |
missense |
probably benign |
0.19 |
|
R7880:Lrrc4c
|
UTSW |
2 |
97,461,143 (GRCm39) |
missense |
probably benign |
0.08 |
|
R8008:Lrrc4c
|
UTSW |
2 |
97,460,594 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R8479:Lrrc4c
|
UTSW |
2 |
97,459,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8802:Lrrc4c
|
UTSW |
2 |
97,460,603 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R8821:Lrrc4c
|
UTSW |
2 |
97,460,040 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R8906:Lrrc4c
|
UTSW |
2 |
97,460,393 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8933:Lrrc4c
|
UTSW |
2 |
97,459,826 (GRCm39) |
missense |
probably benign |
0.36 |
|
R8974:Lrrc4c
|
UTSW |
2 |
97,459,992 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9115:Lrrc4c
|
UTSW |
2 |
97,459,686 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9266:Lrrc4c
|
UTSW |
2 |
97,459,853 (GRCm39) |
missense |
probably benign |
0.26 |
|
R9311:Lrrc4c
|
UTSW |
2 |
97,461,080 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
Z1177:Lrrc4c
|
UTSW |
2 |
97,460,828 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ACAGCGGAATCCCAGGAATTGATG -3'
(R):5'- AGACTGGATCTCACCACTAGAATTCACC -3'
Sequencing Primer
(F):5'- ATCCCAGGAATTGATGAGGTC -3'
(R):5'- atttagcccagtcatttgtgtc -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation