Incidental Mutation 'IGL01112:Ltb'
| ID |
53071 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Ltb
|
| Ensembl Gene |
ENSMUSG00000024399 |
| Gene Name |
lymphotoxin B |
| Synonyms |
p33, Tnfc, lymphotoxin beta, LTbeta, Tnfsf3 |
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.097)
|
| Stock # |
IGL01112
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
17 |
| Chromosomal Location |
35413483-35415281 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 35413576 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 27
(T27A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000025262
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025262]
[ENSMUST00000025263]
[ENSMUST00000167924]
[ENSMUST00000173600]
|
| AlphaFold |
P41155 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025262
AA Change: T27A
PolyPhen 2
Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000025262
Gene: ENSMUSG00000024399
AA Change: T27A
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
21 |
43 |
N/A |
INTRINSIC |
|
low complexity region
|
72 |
85 |
N/A |
INTRINSIC |
|
TNF
|
154 |
305 |
8.76e-42 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025263
|
| SMART Domains |
Protein: ENSMUSP00000025263
Gene: ENSMUSG00000024401
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
35 |
57 |
N/A |
INTRINSIC |
|
TNF
|
91 |
235 |
1.59e-53 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000167924
|
| SMART Domains |
Protein: ENSMUSP00000126122
Gene: ENSMUSG00000024401
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
35 |
57 |
N/A |
INTRINSIC |
|
TNF
|
74 |
219 |
2.8e-49 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173510
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173600
|
| SMART Domains |
Protein: ENSMUSP00000134706
Gene: ENSMUSG00000024399
| Domain | Start | End | E-Value | Type |
|---|
|
TNF
|
33 |
184 |
8.76e-42 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183646
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations lack peripheral lymph nodes, Peyer's patches, splenic germinal centers and follicular dendritic cells. Mutants exhibit lymphocytosis in the circulation and peritoneal cavity with infiltrations of the lung and liver. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ano1 |
T |
C |
7: 144,190,882 (GRCm39) |
I401V |
possibly damaging |
Het |
| Ap2a2 |
A |
T |
7: 141,184,932 (GRCm39) |
|
probably benign |
Het |
| Apol7c |
T |
A |
15: 77,410,637 (GRCm39) |
D103V |
probably damaging |
Het |
| Arid4a |
T |
C |
12: 71,119,507 (GRCm39) |
|
probably null |
Het |
| Atp2a1 |
A |
G |
7: 126,049,479 (GRCm39) |
V521A |
probably benign |
Het |
| Ccdc88c |
G |
T |
12: 100,883,062 (GRCm39) |
D1603E |
probably benign |
Het |
| Clec4f |
T |
C |
6: 83,630,182 (GRCm39) |
I125M |
probably benign |
Het |
| Dsc1 |
T |
C |
18: 20,227,679 (GRCm39) |
I520V |
probably benign |
Het |
| Eomes |
G |
A |
9: 118,311,334 (GRCm39) |
A386T |
probably damaging |
Het |
| Gldc |
C |
T |
19: 30,135,913 (GRCm39) |
|
probably null |
Het |
| Hectd4 |
G |
T |
5: 121,445,013 (GRCm39) |
M1420I |
probably benign |
Het |
| Hmcn1 |
A |
T |
1: 150,508,303 (GRCm39) |
|
probably benign |
Het |
| Ighv6-3 |
G |
A |
12: 114,355,335 (GRCm39) |
T118I |
possibly damaging |
Het |
| Krt82 |
A |
G |
15: 101,453,958 (GRCm39) |
F250S |
probably damaging |
Het |
| Mex3b |
T |
A |
7: 82,518,911 (GRCm39) |
S409T |
probably benign |
Het |
| Mki67 |
A |
T |
7: 135,315,745 (GRCm39) |
I39N |
probably damaging |
Het |
| Or51a7 |
A |
G |
7: 102,615,235 (GRCm39) |
|
probably benign |
Het |
| Palmd |
A |
G |
3: 116,717,922 (GRCm39) |
S192P |
probably damaging |
Het |
| Pcdh20 |
A |
T |
14: 88,704,636 (GRCm39) |
M888K |
probably benign |
Het |
| Pclo |
A |
T |
5: 14,731,083 (GRCm39) |
H3195L |
unknown |
Het |
| Pgm2 |
A |
T |
5: 64,260,225 (GRCm39) |
I137F |
possibly damaging |
Het |
| Polq |
T |
A |
16: 36,837,671 (GRCm39) |
N194K |
probably damaging |
Het |
| Rmnd1 |
T |
C |
10: 4,360,793 (GRCm39) |
|
probably null |
Het |
| Rnf114 |
T |
C |
2: 167,354,459 (GRCm39) |
M180T |
probably damaging |
Het |
| Sap30 |
A |
G |
8: 57,938,123 (GRCm39) |
F165L |
possibly damaging |
Het |
| Scgb3a2 |
T |
A |
18: 43,900,059 (GRCm39) |
|
probably benign |
Het |
| Sftpa1 |
A |
T |
14: 40,854,527 (GRCm39) |
N38I |
probably benign |
Het |
| Sumf1 |
A |
G |
6: 108,152,977 (GRCm39) |
F137S |
probably damaging |
Het |
| Tln2 |
C |
A |
9: 67,219,093 (GRCm39) |
R284L |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,570,703 (GRCm39) |
R26730Q |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,540,808 (GRCm39) |
R25732S |
probably damaging |
Het |
| Tubgcp4 |
T |
C |
2: 121,004,082 (GRCm39) |
V41A |
probably benign |
Het |
| Usp53 |
T |
A |
3: 122,751,367 (GRCm39) |
Q230L |
probably damaging |
Het |
| Vmn2r57 |
T |
C |
7: 41,074,467 (GRCm39) |
E532G |
probably damaging |
Het |
| Vps9d1 |
G |
T |
8: 123,972,769 (GRCm39) |
N454K |
probably damaging |
Het |
| Wdr55 |
T |
C |
18: 36,895,132 (GRCm39) |
|
probably null |
Het |
| Zfp263 |
T |
A |
16: 3,566,776 (GRCm39) |
C76S |
probably benign |
Het |
|
| Other mutations in Ltb |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00944:Ltb
|
APN |
17 |
35,413,642 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
IGL02263:Ltb
|
APN |
17 |
35,414,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02983:Ltb
|
APN |
17 |
35,413,646 (GRCm39) |
missense |
probably benign |
0.15 |
|
IGL02995:Ltb
|
APN |
17 |
35,414,348 (GRCm39) |
splice site |
probably benign |
|
|
IGL03389:Ltb
|
APN |
17 |
35,414,044 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0103:Ltb
|
UTSW |
17 |
35,414,016 (GRCm39) |
intron |
probably benign |
|
|
R0103:Ltb
|
UTSW |
17 |
35,414,016 (GRCm39) |
intron |
probably benign |
|
|
R2060:Ltb
|
UTSW |
17 |
35,414,739 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4718:Ltb
|
UTSW |
17 |
35,414,313 (GRCm39) |
splice site |
probably null |
|
|
R4823:Ltb
|
UTSW |
17 |
35,414,206 (GRCm39) |
missense |
probably benign |
|
|
R4884:Ltb
|
UTSW |
17 |
35,414,234 (GRCm39) |
missense |
probably benign |
|
|
R5231:Ltb
|
UTSW |
17 |
35,414,802 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5327:Ltb
|
UTSW |
17 |
35,414,935 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8297:Ltb
|
UTSW |
17 |
35,413,655 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8344:Ltb
|
UTSW |
17 |
35,414,169 (GRCm39) |
missense |
probably benign |
0.41 |
|
R9778:Ltb
|
UTSW |
17 |
35,414,906 (GRCm39) |
nonsense |
probably null |
|
|
| Posted On |
2013-06-21 |
Incidental Mutation