Incidental Mutation 'R6347:Lcp2'
| ID |
520067 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lcp2
|
| Ensembl Gene |
ENSMUSG00000002699 |
| Gene Name |
lymphocyte cytosolic protein 2 |
| Synonyms |
m1Khoe, SLP-76, SLP76, twm |
| MMRRC Submission |
044501-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6347 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
33996928-34042281 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 34032501 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Valine
at position 360
(M360V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000104952
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000052413]
[ENSMUST00000109329]
|
| AlphaFold |
Q60787 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000052413
AA Change: M360V
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000056621
Gene: ENSMUSG00000002699
AA Change: M360V
| Domain | Start | End | E-Value | Type |
|---|
|
SAM
|
12 |
78 |
9.3e-4 |
SMART |
|
low complexity region
|
109 |
127 |
N/A |
INTRINSIC |
|
low complexity region
|
186 |
201 |
N/A |
INTRINSIC |
|
low complexity region
|
204 |
222 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
274 |
321 |
1.93e-5 |
PROSPERO |
|
low complexity region
|
328 |
339 |
N/A |
INTRINSIC |
|
low complexity region
|
400 |
412 |
N/A |
INTRINSIC |
|
SH2
|
421 |
512 |
4.44e-25 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000109329
AA Change: M360V
PolyPhen 2
Score 0.104 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000104952
Gene: ENSMUSG00000002699
AA Change: M360V
| Domain | Start | End | E-Value | Type |
|---|
|
SAM
|
12 |
78 |
9.3e-4 |
SMART |
|
low complexity region
|
109 |
127 |
N/A |
INTRINSIC |
|
low complexity region
|
186 |
201 |
N/A |
INTRINSIC |
|
low complexity region
|
204 |
222 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
274 |
321 |
1.86e-5 |
PROSPERO |
|
low complexity region
|
328 |
339 |
N/A |
INTRINSIC |
|
low complexity region
|
400 |
412 |
N/A |
INTRINSIC |
|
SH2
|
421 |
508 |
8.9e-16 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133120
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141450
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146318
|
| Meta Mutation Damage Score |
0.0904 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.6%
- 20x: 92.3%
|
| Validation Efficiency |
95% (41/43) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]
PHENOTYPE: T cell development is blocked and T cell receptor signaling impaired in homozygous point mutants. Double positive thymocyte and single positive T cell numbers are much reduced. Both positive and negative thymocyte selection is abnormal. Mice have high IgG and IgE levels and exhibit autoimmunity. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atat1 |
A |
G |
17: 36,220,921 (GRCm39) |
F3L |
probably damaging |
Het |
| Atf7 |
T |
A |
15: 102,454,914 (GRCm39) |
M285L |
possibly damaging |
Het |
| Bcl7b |
T |
C |
5: 135,209,387 (GRCm39) |
S95P |
possibly damaging |
Het |
| Cald1 |
A |
C |
6: 34,741,981 (GRCm39) |
K453Q |
probably damaging |
Het |
| Cimip1 |
G |
T |
2: 173,369,708 (GRCm39) |
R74L |
possibly damaging |
Het |
| Cog4 |
A |
T |
8: 111,607,275 (GRCm39) |
I580F |
probably damaging |
Het |
| Cpq |
T |
A |
15: 33,290,332 (GRCm39) |
|
probably null |
Het |
| Csf2rb |
G |
A |
15: 78,229,752 (GRCm39) |
D440N |
probably damaging |
Het |
| Dst |
A |
G |
1: 34,218,765 (GRCm39) |
|
probably null |
Het |
| Eif2b3 |
T |
C |
4: 116,901,763 (GRCm39) |
V142A |
probably benign |
Het |
| Fat3 |
A |
T |
9: 15,909,668 (GRCm39) |
N2111K |
probably damaging |
Het |
| Fbxo31 |
C |
A |
8: 122,305,198 (GRCm39) |
E99D |
possibly damaging |
Het |
| Fgfr2 |
T |
C |
7: 129,863,487 (GRCm39) |
E34G |
probably damaging |
Het |
| Flvcr2 |
T |
C |
12: 85,794,194 (GRCm39) |
V190A |
possibly damaging |
Het |
| Herc2 |
T |
C |
7: 55,844,151 (GRCm39) |
|
probably null |
Het |
| Igkv3-2 |
A |
C |
6: 70,676,017 (GRCm39) |
M109L |
probably benign |
Het |
| Il36rn |
G |
A |
2: 24,169,726 (GRCm39) |
A29T |
probably damaging |
Het |
| Kif13b |
C |
T |
14: 65,005,068 (GRCm39) |
T1120I |
probably benign |
Het |
| Kmt2c |
A |
G |
5: 25,515,833 (GRCm39) |
I2670T |
possibly damaging |
Het |
| Ldlrad4 |
A |
G |
18: 68,368,851 (GRCm39) |
S103G |
probably benign |
Het |
| Loxl4 |
T |
C |
19: 42,596,709 (GRCm39) |
K88E |
probably damaging |
Het |
| Ltbp2 |
C |
A |
12: 84,900,686 (GRCm39) |
R192L |
probably damaging |
Het |
| Mast2 |
C |
A |
4: 116,174,929 (GRCm39) |
G475V |
probably damaging |
Het |
| Meis1 |
A |
C |
11: 18,855,631 (GRCm39) |
|
probably null |
Het |
| Mroh3 |
T |
C |
1: 136,128,675 (GRCm39) |
|
probably null |
Het |
| Myo5b |
C |
T |
18: 74,903,456 (GRCm39) |
A1824V |
probably benign |
Het |
| Nectin3 |
C |
T |
16: 46,278,487 (GRCm39) |
V303M |
probably benign |
Het |
| Or5p52 |
T |
C |
7: 107,502,157 (GRCm39) |
S78P |
possibly damaging |
Het |
| Peak1 |
T |
C |
9: 56,165,495 (GRCm39) |
N811S |
probably benign |
Het |
| Pik3ca |
C |
T |
3: 32,516,970 (GRCm39) |
A1066V |
probably benign |
Het |
| Rnf103 |
A |
G |
6: 71,482,808 (GRCm39) |
T153A |
possibly damaging |
Het |
| Sacs |
G |
A |
14: 61,448,609 (GRCm39) |
V3552I |
probably damaging |
Het |
| Sgca |
A |
T |
11: 94,862,854 (GRCm39) |
N109K |
probably damaging |
Het |
| Speg |
T |
A |
1: 75,403,519 (GRCm39) |
M2621K |
probably benign |
Het |
| Stfa2l1 |
T |
C |
16: 35,977,271 (GRCm39) |
I22T |
probably damaging |
Het |
| Tbpl2 |
G |
A |
2: 23,984,715 (GRCm39) |
P144L |
probably benign |
Het |
| Tmem219 |
T |
C |
7: 126,495,998 (GRCm39) |
N119S |
possibly damaging |
Het |
| Ush2a |
A |
G |
1: 188,643,084 (GRCm39) |
T4149A |
probably benign |
Het |
| Wdr46 |
C |
A |
17: 34,160,826 (GRCm39) |
P197T |
probably damaging |
Het |
| Wee2 |
C |
T |
6: 40,432,039 (GRCm39) |
R203C |
probably damaging |
Het |
|
| Other mutations in Lcp2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01451:Lcp2
|
APN |
11 |
33,997,345 (GRCm39) |
start gained |
probably benign |
|
|
IGL01730:Lcp2
|
APN |
11 |
34,000,943 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL02174:Lcp2
|
APN |
11 |
34,000,966 (GRCm39) |
splice site |
probably benign |
|
|
IGL02228:Lcp2
|
APN |
11 |
33,997,424 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02814:Lcp2
|
APN |
11 |
34,021,033 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0142:Lcp2
|
UTSW |
11 |
34,032,418 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0277:Lcp2
|
UTSW |
11 |
34,004,322 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0281:Lcp2
|
UTSW |
11 |
34,019,854 (GRCm39) |
splice site |
probably benign |
|
|
R0323:Lcp2
|
UTSW |
11 |
34,004,322 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0437:Lcp2
|
UTSW |
11 |
34,037,229 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0632:Lcp2
|
UTSW |
11 |
34,032,426 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R1479:Lcp2
|
UTSW |
11 |
34,025,068 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1570:Lcp2
|
UTSW |
11 |
34,039,601 (GRCm39) |
missense |
probably benign |
0.07 |
|
R1744:Lcp2
|
UTSW |
11 |
34,019,911 (GRCm39) |
splice site |
probably null |
|
|
R2212:Lcp2
|
UTSW |
11 |
34,020,995 (GRCm39) |
missense |
probably benign |
0.14 |
|
R2910:Lcp2
|
UTSW |
11 |
34,018,970 (GRCm39) |
splice site |
probably null |
|
|
R2911:Lcp2
|
UTSW |
11 |
34,018,970 (GRCm39) |
splice site |
probably null |
|
|
R3196:Lcp2
|
UTSW |
11 |
34,040,670 (GRCm39) |
missense |
probably benign |
0.05 |
|
R4012:Lcp2
|
UTSW |
11 |
34,018,439 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4411:Lcp2
|
UTSW |
11 |
34,037,173 (GRCm39) |
unclassified |
probably benign |
|
|
R4417:Lcp2
|
UTSW |
11 |
34,000,917 (GRCm39) |
missense |
probably benign |
0.27 |
|
R4423:Lcp2
|
UTSW |
11 |
34,028,226 (GRCm39) |
intron |
probably benign |
|
|
R4718:Lcp2
|
UTSW |
11 |
34,020,992 (GRCm39) |
missense |
probably benign |
0.09 |
|
R5090:Lcp2
|
UTSW |
11 |
34,039,725 (GRCm39) |
nonsense |
probably null |
|
|
R7315:Lcp2
|
UTSW |
11 |
34,019,906 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7694:Lcp2
|
UTSW |
11 |
34,000,924 (GRCm39) |
missense |
probably benign |
0.16 |
|
R7910:Lcp2
|
UTSW |
11 |
34,038,061 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8325:Lcp2
|
UTSW |
11 |
34,032,394 (GRCm39) |
missense |
probably benign |
0.34 |
|
R8435:Lcp2
|
UTSW |
11 |
34,004,316 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8709:Lcp2
|
UTSW |
11 |
34,004,354 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R9091:Lcp2
|
UTSW |
11 |
34,039,688 (GRCm39) |
missense |
|
|
|
R9270:Lcp2
|
UTSW |
11 |
34,039,688 (GRCm39) |
missense |
|
|
|
R9566:Lcp2
|
UTSW |
11 |
34,000,944 (GRCm39) |
missense |
|
|
|
| Predicted Primers |
PCR Primer
(F):5'- TTCATGTCAGCTGGGTTTGA -3'
(R):5'- CTGGTGTTTGCCGTAGCTAAGT -3'
Sequencing Primer
(F):5'- CATGTCAGCTGGGTTTGATTTAAG -3'
(R):5'- GAGTACACTGTGGCTAGCTAC -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation