Incidental Mutation 'R1689:Pdlim2'
ID |
189597 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdlim2
|
Ensembl Gene |
ENSMUSG00000022090 |
Gene Name |
PDZ and LIM domain 2 |
Synonyms |
SLIM, 4732462F18Rik, mystique |
MMRRC Submission |
039722-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.074)
|
Stock # |
R1689 (G1)
|
Quality Score |
179 |
Status
|
Not validated
|
Chromosome |
14 |
Chromosomal Location |
70401667-70415130 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 70408688 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glycine to Aspartic acid
at position 176
(G176D)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116200
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000022681]
[ENSMUST00000127836]
[ENSMUST00000129174]
[ENSMUST00000143393]
[ENSMUST00000153735]
|
AlphaFold |
Q8R1G6 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000022681
AA Change: G176D
PolyPhen 2
Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000022681 Gene: ENSMUSG00000022090 AA Change: G176D
Domain | Start | End | E-Value | Type |
PDZ
|
11 |
84 |
3.41e-17 |
SMART |
low complexity region
|
129 |
144 |
N/A |
INTRINSIC |
Pfam:DUF4749
|
169 |
256 |
4.4e-12 |
PFAM |
low complexity region
|
259 |
271 |
N/A |
INTRINSIC |
LIM
|
282 |
334 |
1.25e-6 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123125
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000125300
|
SMART Domains |
Protein: ENSMUSP00000116694 Gene: ENSMUSG00000022090
Domain | Start | End | E-Value | Type |
Pfam:DUF4749
|
7 |
58 |
6.4e-13 |
PFAM |
low complexity region
|
61 |
73 |
N/A |
INTRINSIC |
LIM
|
84 |
136 |
1.25e-6 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000127836
|
SMART Domains |
Protein: ENSMUSP00000141050 Gene: ENSMUSG00000022090
Domain | Start | End | E-Value | Type |
low complexity region
|
20 |
29 |
N/A |
INTRINSIC |
low complexity region
|
38 |
50 |
N/A |
INTRINSIC |
LIM
|
61 |
113 |
5.9e-9 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000129174
|
SMART Domains |
Protein: ENSMUSP00000139820 Gene: ENSMUSG00000022090
Domain | Start | End | E-Value | Type |
low complexity region
|
20 |
29 |
N/A |
INTRINSIC |
low complexity region
|
38 |
50 |
N/A |
INTRINSIC |
LIM
|
61 |
113 |
5.9e-9 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135944
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000143393
AA Change: G176D
PolyPhen 2
Score 0.546 (Sensitivity: 0.88; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000119222 Gene: ENSMUSG00000022090 AA Change: G176D
Domain | Start | End | E-Value | Type |
PDZ
|
11 |
84 |
3.41e-17 |
SMART |
low complexity region
|
129 |
144 |
N/A |
INTRINSIC |
low complexity region
|
199 |
210 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000153735
AA Change: G176D
PolyPhen 2
Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000116200 Gene: ENSMUSG00000022090 AA Change: G176D
Domain | Start | End | E-Value | Type |
PDZ
|
11 |
84 |
3.41e-17 |
SMART |
low complexity region
|
129 |
144 |
N/A |
INTRINSIC |
low complexity region
|
199 |
210 |
N/A |
INTRINSIC |
low complexity region
|
241 |
250 |
N/A |
INTRINSIC |
low complexity region
|
259 |
271 |
N/A |
INTRINSIC |
LIM
|
282 |
334 |
1.25e-6 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141363
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138792
|
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.9%
|
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 ALP subfamily of PDZ-LIM domain proteins. The encoded protein suppresses anchorage-dependent growth and promotes cell migration and adhesion through interactions with the actin cytoskeleton via the PDZ domain. The encoded protein is also a putative tumor suppressor protein, and decreased expression of this gene is associated with several malignancies including breast cancer and adult T-cell leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011] PHENOTYPE: Mice homozygous for a knock-out allele display increased IFN-gamma production by Th1 cells and an enhanced inflammatory response to in vivo challenge with heat-killed Listeria monocytogenes. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 66 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcc8 |
T |
C |
7: 45,769,827 (GRCm39) |
K896R |
probably benign |
Het |
Adcy9 |
A |
T |
16: 4,115,426 (GRCm39) |
|
probably null |
Het |
Adgre1 |
T |
C |
17: 57,756,921 (GRCm39) |
F726S |
probably benign |
Het |
Ahctf1 |
A |
T |
1: 179,595,948 (GRCm39) |
S148T |
probably damaging |
Het |
Aif1 |
G |
A |
17: 35,391,127 (GRCm39) |
P44L |
probably benign |
Het |
Ammecr1l |
C |
A |
18: 31,913,741 (GRCm39) |
A289D |
probably benign |
Het |
Amotl1 |
T |
C |
9: 14,504,518 (GRCm39) |
Y230C |
probably damaging |
Het |
Armc6 |
A |
T |
8: 70,682,187 (GRCm39) |
S65R |
probably benign |
Het |
Atad2b |
T |
A |
12: 5,084,575 (GRCm39) |
Y1440* |
probably null |
Het |
Atf6b |
T |
A |
17: 34,869,276 (GRCm39) |
D164E |
probably damaging |
Het |
B4galt6 |
C |
T |
18: 20,839,553 (GRCm39) |
S127N |
probably benign |
Het |
Bcl11a |
A |
T |
11: 24,113,167 (GRCm39) |
Y170F |
probably damaging |
Het |
Bcl11a |
A |
T |
11: 24,114,406 (GRCm39) |
D583V |
possibly damaging |
Het |
Btnl1 |
T |
A |
17: 34,600,182 (GRCm39) |
Y228* |
probably null |
Het |
Cav2 |
A |
G |
6: 17,281,421 (GRCm39) |
H21R |
probably benign |
Het |
Celsr2 |
T |
A |
3: 108,314,620 (GRCm39) |
D1135V |
possibly damaging |
Het |
Cntnap1 |
A |
C |
11: 101,079,699 (GRCm39) |
|
probably null |
Het |
Cysltr2 |
T |
C |
14: 73,267,470 (GRCm39) |
D80G |
possibly damaging |
Het |
Dclk2 |
C |
T |
3: 86,712,946 (GRCm39) |
R503Q |
possibly damaging |
Het |
Dgkh |
A |
T |
14: 78,855,984 (GRCm39) |
M363K |
possibly damaging |
Het |
Eml5 |
C |
T |
12: 98,797,194 (GRCm39) |
V1112M |
probably damaging |
Het |
Entpd7 |
A |
G |
19: 43,713,915 (GRCm39) |
T425A |
probably damaging |
Het |
Ephx2 |
T |
A |
14: 66,324,475 (GRCm39) |
K373* |
probably null |
Het |
F5 |
G |
C |
1: 164,026,486 (GRCm39) |
R1686P |
probably damaging |
Het |
Fbxw10 |
A |
T |
11: 62,750,862 (GRCm39) |
I482L |
probably damaging |
Het |
Fbxw8 |
T |
C |
5: 118,215,682 (GRCm39) |
S443G |
probably damaging |
Het |
Fdft1 |
T |
C |
14: 63,394,138 (GRCm39) |
E191G |
probably benign |
Het |
Fgd2 |
A |
G |
17: 29,582,696 (GRCm39) |
E26G |
probably benign |
Het |
Gabra4 |
T |
C |
5: 71,790,885 (GRCm39) |
|
probably null |
Het |
Gc |
A |
G |
5: 89,589,059 (GRCm39) |
|
probably null |
Het |
Heatr1 |
T |
A |
13: 12,439,506 (GRCm39) |
D1361E |
probably benign |
Het |
Hid1 |
A |
G |
11: 115,251,183 (GRCm39) |
F118L |
probably damaging |
Het |
Igsf8 |
G |
T |
1: 172,146,504 (GRCm39) |
G564W |
probably damaging |
Het |
Il12rb2 |
A |
G |
6: 67,313,744 (GRCm39) |
V4A |
probably benign |
Het |
Irak3 |
T |
C |
10: 119,982,457 (GRCm39) |
E335G |
probably damaging |
Het |
Itgb8 |
T |
G |
12: 119,134,555 (GRCm39) |
Q504P |
probably benign |
Het |
Kbtbd12 |
A |
T |
6: 88,595,567 (GRCm39) |
Y88N |
probably damaging |
Het |
Klk1b5 |
T |
C |
7: 43,869,969 (GRCm39) |
I226T |
probably damaging |
Het |
L3hypdh |
A |
T |
12: 72,131,527 (GRCm39) |
I135N |
probably damaging |
Het |
Lrp2 |
G |
T |
2: 69,333,873 (GRCm39) |
T1456K |
probably benign |
Het |
Mrgprd |
C |
A |
7: 144,875,454 (GRCm39) |
Y108* |
probably null |
Het |
Muc6 |
C |
T |
7: 141,234,265 (GRCm39) |
G742D |
probably damaging |
Het |
Nalcn |
T |
A |
14: 123,522,666 (GRCm39) |
I1572F |
probably damaging |
Het |
Nceh1 |
A |
G |
3: 27,280,231 (GRCm39) |
Y126C |
probably damaging |
Het |
Or14j1 |
T |
C |
17: 38,146,495 (GRCm39) |
S202P |
possibly damaging |
Het |
Or1ak2 |
A |
G |
2: 36,827,989 (GRCm39) |
N286S |
probably damaging |
Het |
Or7d11 |
A |
T |
9: 19,966,422 (GRCm39) |
N112K |
possibly damaging |
Het |
Pacs1 |
G |
T |
19: 5,322,643 (GRCm39) |
|
probably benign |
Het |
Pappa2 |
A |
G |
1: 158,784,968 (GRCm39) |
L14P |
probably damaging |
Het |
Pramel17 |
T |
A |
4: 101,694,376 (GRCm39) |
K169I |
possibly damaging |
Het |
Ptpra |
T |
C |
2: 130,345,412 (GRCm39) |
F5L |
probably benign |
Het |
Qrfprl |
A |
G |
6: 65,358,591 (GRCm39) |
N105S |
possibly damaging |
Het |
Ralgapa1 |
A |
G |
12: 55,723,552 (GRCm39) |
L2114P |
possibly damaging |
Het |
Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
Senp2 |
T |
A |
16: 21,845,416 (GRCm39) |
Y217N |
probably damaging |
Het |
Sned1 |
C |
T |
1: 93,211,094 (GRCm39) |
R1061C |
probably damaging |
Het |
Spag16 |
C |
T |
1: 70,500,277 (GRCm39) |
T535I |
probably benign |
Het |
Supt20 |
T |
A |
3: 54,619,583 (GRCm39) |
L355* |
probably null |
Het |
Tmem132b |
A |
G |
5: 125,864,678 (GRCm39) |
H928R |
possibly damaging |
Het |
Tpo |
A |
T |
12: 30,148,245 (GRCm39) |
L552H |
probably damaging |
Het |
Tsfm |
A |
T |
10: 126,864,324 (GRCm39) |
N130K |
probably damaging |
Het |
Usp48 |
T |
A |
4: 137,383,418 (GRCm39) |
|
probably null |
Het |
Vsig10 |
A |
G |
5: 117,490,825 (GRCm39) |
D544G |
probably benign |
Het |
Vsig10l |
C |
T |
7: 43,114,792 (GRCm39) |
T433I |
possibly damaging |
Het |
Wdr81 |
A |
G |
11: 75,336,422 (GRCm39) |
F1655L |
probably damaging |
Het |
Wfdc3 |
T |
A |
2: 164,576,111 (GRCm39) |
D60V |
probably damaging |
Het |
|
Other mutations in Pdlim2 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL02295:Pdlim2
|
APN |
14 |
70,403,532 (GRCm39) |
splice site |
probably benign |
|
IGL02338:Pdlim2
|
APN |
14 |
70,411,906 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03286:Pdlim2
|
APN |
14 |
70,411,925 (GRCm39) |
missense |
possibly damaging |
0.88 |
PIT4504001:Pdlim2
|
UTSW |
14 |
70,403,579 (GRCm39) |
missense |
probably benign |
0.44 |
R0751:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R0768:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R0832:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1167:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1207:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1207:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1343:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1412:Pdlim2
|
UTSW |
14 |
70,411,773 (GRCm39) |
splice site |
probably benign |
|
R1595:Pdlim2
|
UTSW |
14 |
70,402,193 (GRCm39) |
missense |
probably damaging |
1.00 |
R1703:Pdlim2
|
UTSW |
14 |
70,411,784 (GRCm39) |
critical splice donor site |
probably null |
|
R1843:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1845:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1923:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1924:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R1925:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R2004:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R2005:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R2202:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R2205:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R2237:Pdlim2
|
UTSW |
14 |
70,408,698 (GRCm39) |
missense |
probably benign |
0.05 |
R2843:Pdlim2
|
UTSW |
14 |
70,403,549 (GRCm39) |
missense |
probably benign |
0.02 |
R4042:Pdlim2
|
UTSW |
14 |
70,402,228 (GRCm39) |
missense |
probably damaging |
1.00 |
R4965:Pdlim2
|
UTSW |
14 |
70,405,464 (GRCm39) |
unclassified |
probably benign |
|
R4971:Pdlim2
|
UTSW |
14 |
70,405,208 (GRCm39) |
missense |
probably damaging |
1.00 |
R5951:Pdlim2
|
UTSW |
14 |
70,405,229 (GRCm39) |
missense |
probably benign |
0.06 |
R6252:Pdlim2
|
UTSW |
14 |
70,405,137 (GRCm39) |
missense |
probably damaging |
1.00 |
R7208:Pdlim2
|
UTSW |
14 |
70,411,826 (GRCm39) |
missense |
probably damaging |
1.00 |
R7597:Pdlim2
|
UTSW |
14 |
70,403,645 (GRCm39) |
missense |
possibly damaging |
0.58 |
R7627:Pdlim2
|
UTSW |
14 |
70,408,924 (GRCm39) |
missense |
probably benign |
|
R8342:Pdlim2
|
UTSW |
14 |
70,403,563 (GRCm39) |
missense |
probably damaging |
1.00 |
R8554:Pdlim2
|
UTSW |
14 |
70,408,698 (GRCm39) |
missense |
probably benign |
|
R9361:Pdlim2
|
UTSW |
14 |
70,402,190 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- GACTGCAAGTGGCCTCAGTGTTAG -3'
(R):5'- TGGCAACCAGATTCCAGGTAAGC -3'
Sequencing Primer
(F):5'- TGTTAGCTAGCTTCTCTGGC -3'
(R):5'- ctaccagcccagttgcc -3'
|
Posted On |
2014-05-14 |