Incidental Mutation 'R2353:Lrrc4'
| ID |
246252 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrrc4
|
| Ensembl Gene |
ENSMUSG00000049939 |
| Gene Name |
leucine rich repeat containing 4 |
| Synonyms |
Nag14, NGL-2, NGL2 |
| MMRRC Submission |
040335-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.201)
|
| Stock # |
R2353 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
28828125-28831746 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 28831451 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 55
(F55L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000062158
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001460]
[ENSMUST00000062304]
[ENSMUST00000164915]
[ENSMUST00000167201]
[ENSMUST00000171353]
|
| AlphaFold |
Q99PH1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001460
|
| SMART Domains |
Protein: ENSMUSP00000001460
Gene: ENSMUSG00000001424
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
15 |
N/A |
INTRINSIC |
|
SNc
|
18 |
166 |
7.12e-54 |
SMART |
|
SNc
|
193 |
328 |
8.37e-51 |
SMART |
|
SNc
|
341 |
496 |
4.11e-59 |
SMART |
|
SNc
|
525 |
660 |
3.82e-45 |
SMART |
|
TUDOR
|
728 |
785 |
4.8e-19 |
SMART |
|
Pfam:SNase
|
835 |
895 |
1.3e-7 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000062304
AA Change: F55L
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: F55L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
32 |
40 |
N/A |
INTRINSIC |
|
LRRNT
|
44 |
78 |
4.05e-5 |
SMART |
|
LRR
|
72 |
96 |
1.19e2 |
SMART |
|
LRR_TYP
|
97 |
120 |
2.24e-3 |
SMART |
|
LRR
|
121 |
144 |
6.13e-1 |
SMART |
|
LRR_TYP
|
145 |
168 |
5.99e-4 |
SMART |
|
LRR
|
216 |
239 |
1.25e-1 |
SMART |
|
LRR
|
240 |
263 |
4.71e1 |
SMART |
|
LRR_TYP
|
264 |
287 |
2.79e-4 |
SMART |
|
LRRCT
|
299 |
350 |
8.06e-6 |
SMART |
|
IGc2
|
364 |
430 |
5.24e-7 |
SMART |
|
low complexity region
|
452 |
462 |
N/A |
INTRINSIC |
|
transmembrane domain
|
527 |
549 |
N/A |
INTRINSIC |
|
low complexity region
|
575 |
586 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164915
|
| SMART Domains |
Protein: ENSMUSP00000127317
Gene: ENSMUSG00000001424
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
15 |
N/A |
INTRINSIC |
|
SNc
|
18 |
142 |
1.56e-18 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000167201
|
| SMART Domains |
Protein: ENSMUSP00000128737
Gene: ENSMUSG00000001424
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
15 |
N/A |
INTRINSIC |
|
SNc
|
18 |
166 |
7.12e-54 |
SMART |
|
SNc
|
193 |
328 |
8.37e-51 |
SMART |
|
SNc
|
341 |
496 |
4.11e-59 |
SMART |
|
SCOP:d1sty__
|
526 |
592 |
1e-4 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169579
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000171195
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000171353
|
| SMART Domains |
Protein: ENSMUSP00000129497
Gene: ENSMUSG00000049939
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
29 |
39 |
N/A |
INTRINSIC |
|
transmembrane domain
|
104 |
126 |
N/A |
INTRINSIC |
|
low complexity region
|
152 |
163 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0868 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.2%
|
| Validation Efficiency |
100% (32/32) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is significantly downregulated in primary brain tumors. The exact function of the protein encoded by this gene is unknown. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit hyperactivity, an absence of startle reflex, and abnormal ABR amplitude. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 31 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl4 |
G |
T |
4: 144,349,779 (GRCm39) |
E345D |
probably damaging |
Het |
| Adam7 |
T |
A |
14: 68,742,537 (GRCm39) |
Q692L |
probably benign |
Het |
| Ankk1 |
A |
C |
9: 49,329,990 (GRCm39) |
C322G |
probably benign |
Het |
| Ap3b2 |
C |
T |
7: 81,123,598 (GRCm39) |
|
probably benign |
Het |
| Apeh |
T |
C |
9: 107,963,491 (GRCm39) |
D577G |
possibly damaging |
Het |
| Aspm |
T |
A |
1: 139,405,435 (GRCm39) |
W1441R |
probably damaging |
Het |
| B4galt3 |
C |
A |
1: 171,101,613 (GRCm39) |
H196N |
probably damaging |
Het |
| Cd163 |
G |
T |
6: 124,296,115 (GRCm39) |
E820* |
probably null |
Het |
| Cd38 |
T |
A |
5: 44,065,353 (GRCm39) |
|
probably null |
Het |
| Cdh15 |
G |
A |
8: 123,588,763 (GRCm39) |
R279Q |
probably damaging |
Het |
| Enpp1 |
C |
A |
10: 24,527,239 (GRCm39) |
Q649H |
probably benign |
Het |
| Garnl3 |
T |
A |
2: 32,954,046 (GRCm39) |
R86S |
probably damaging |
Het |
| Gbe1 |
A |
G |
16: 70,233,909 (GRCm39) |
|
probably null |
Het |
| Gm5117 |
A |
G |
8: 32,229,223 (GRCm39) |
|
noncoding transcript |
Het |
| Hip1 |
A |
T |
5: 135,441,566 (GRCm39) |
V568E |
probably damaging |
Het |
| Hspa14 |
G |
A |
2: 3,512,213 (GRCm39) |
|
probably null |
Het |
| Med31 |
T |
A |
11: 72,104,966 (GRCm39) |
N35I |
probably damaging |
Het |
| Msi1 |
C |
A |
5: 115,574,568 (GRCm39) |
|
probably benign |
Het |
| Or1e34 |
T |
C |
11: 73,778,660 (GRCm39) |
I179M |
probably benign |
Het |
| Or4b1 |
A |
T |
2: 89,980,062 (GRCm39) |
L96Q |
probably damaging |
Het |
| Parl |
T |
C |
16: 20,105,790 (GRCm39) |
T211A |
probably benign |
Het |
| Ppwd1 |
T |
C |
13: 104,350,090 (GRCm39) |
I432V |
probably benign |
Het |
| Scn10a |
T |
A |
9: 119,467,753 (GRCm39) |
I796F |
probably damaging |
Het |
| Semp2l2a |
T |
A |
8: 13,886,951 (GRCm39) |
E380V |
probably damaging |
Het |
| Sh3rf3 |
A |
G |
10: 58,842,895 (GRCm39) |
D287G |
probably damaging |
Het |
| Sin3b |
T |
C |
8: 73,450,780 (GRCm39) |
|
probably null |
Het |
| Ubr4 |
T |
C |
4: 139,160,984 (GRCm39) |
I2493T |
possibly damaging |
Het |
| Uts2 |
T |
A |
4: 151,084,593 (GRCm39) |
|
probably null |
Het |
| Zfp109 |
T |
C |
7: 23,928,806 (GRCm39) |
D201G |
probably benign |
Het |
| Zfp407 |
A |
G |
18: 84,578,005 (GRCm39) |
F1036S |
probably damaging |
Het |
| Znrf3 |
T |
C |
11: 5,231,170 (GRCm39) |
E685G |
probably damaging |
Het |
|
| Other mutations in Lrrc4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02230:Lrrc4
|
APN |
6 |
28,830,879 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03223:Lrrc4
|
APN |
6 |
28,831,469 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03410:Lrrc4
|
APN |
6 |
28,830,515 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0233:Lrrc4
|
UTSW |
6 |
28,829,734 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0233:Lrrc4
|
UTSW |
6 |
28,829,734 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0456:Lrrc4
|
UTSW |
6 |
28,831,103 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1162:Lrrc4
|
UTSW |
6 |
28,831,083 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2001:Lrrc4
|
UTSW |
6 |
28,830,904 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2089:Lrrc4
|
UTSW |
6 |
28,830,586 (GRCm39) |
missense |
probably benign |
0.45 |
|
R2091:Lrrc4
|
UTSW |
6 |
28,830,586 (GRCm39) |
missense |
probably benign |
0.45 |
|
R2091:Lrrc4
|
UTSW |
6 |
28,830,586 (GRCm39) |
missense |
probably benign |
0.45 |
|
R5079:Lrrc4
|
UTSW |
6 |
28,830,769 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R5197:Lrrc4
|
UTSW |
6 |
28,830,142 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6701:Lrrc4
|
UTSW |
6 |
28,830,905 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6755:Lrrc4
|
UTSW |
6 |
28,831,292 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7660:Lrrc4
|
UTSW |
6 |
28,829,816 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7661:Lrrc4
|
UTSW |
6 |
28,829,762 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8113:Lrrc4
|
UTSW |
6 |
28,829,902 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8272:Lrrc4
|
UTSW |
6 |
28,662,192 (GRCm39) |
missense |
unknown |
|
|
R9074:Lrrc4
|
UTSW |
6 |
28,831,595 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9094:Lrrc4
|
UTSW |
6 |
28,830,206 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R9197:Lrrc4
|
UTSW |
6 |
28,831,318 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9447:Lrrc4
|
UTSW |
6 |
28,830,650 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9803:Lrrc4
|
UTSW |
6 |
28,662,199 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCTGCCTGATGGAGTTCCTG -3'
(R):5'- AAGGCTGGTTCTCTTTTCCAAGC -3'
Sequencing Primer
(F):5'- TGATGGAGTTCCTGCCCAG -3'
(R):5'- TGGTGAATTATGAACGTGCCACAC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation