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) question?
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
AlleleSourceChrCoordTypePredicted EffectPPH 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