Incidental Mutation 'R1646:Pdlim4'
ID 173895
Institutional Source Beutler Lab
Gene Symbol Pdlim4
Ensembl Gene ENSMUSG00000020388
Gene Name PDZ and LIM domain 4
Synonyms Ril
MMRRC Submission 039682-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.191) question?
Stock # R1646 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 54054928-54069014 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 54056254 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 132 (L132Q)
Ref Sequence ENSEMBL: ENSMUSP00000090797 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018755] [ENSMUST00000093109] [ENSMUST00000144477]
AlphaFold P70271
Predicted Effect possibly damaging
Transcript: ENSMUST00000018755
AA Change: L132Q

PolyPhen 2 Score 0.870 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: L132Q

DomainStartEndE-ValueType
PDZ 11 84 1.05e-17 SMART
Pfam:DUF4749 142 230 7.2e-14 PFAM
LIM 254 305 9.75e-18 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000093109
AA Change: L132Q

PolyPhen 2 Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: L132Q

DomainStartEndE-ValueType
PDZ 11 84 1.05e-17 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127271
Predicted Effect possibly damaging
Transcript: ENSMUST00000144477
AA Change: L73Q

PolyPhen 2 Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388
AA Change: L73Q

DomainStartEndE-ValueType
Blast:PDZ 1 25 2e-10 BLAST
SCOP:d1qava_ 1 25 3e-4 SMART
PDB:2V1W|B 1 28 2e-11 PDB
Meta Mutation Damage Score 0.0851 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.8%
Validation Efficiency 96% (69/72)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5330417C22Rik A T 3: 108,462,990 S751T probably damaging Het
Akna T G 4: 63,383,892 I581L probably benign Het
Cacnb4 A G 2: 52,474,900 I117T possibly damaging Het
Capn1 A T 19: 5,997,730 F434L probably benign Het
Cbs T C 17: 31,613,195 T547A probably benign Het
Col6a5 A T 9: 105,862,749 L2557* probably null Het
D17Wsu92e A G 17: 27,793,960 S88P probably damaging Het
D1Ertd622e A T 1: 97,645,806 I178N probably damaging Het
Dach1 A G 14: 98,169,114 S66P unknown Het
Ddx31 T C 2: 28,892,520 V625A probably benign Het
Dmxl1 T G 18: 49,962,261 V2969G probably damaging Het
Eapp T A 12: 54,685,960 K122* probably null Het
Epb41l5 G T 1: 119,550,022 probably benign Het
Fat1 T C 8: 45,018,042 S1628P probably damaging Het
Fgfr2 T A 7: 130,242,644 E37V probably damaging Het
Fgfr4 A T 13: 55,165,964 N529Y probably damaging Het
Fsip2 A T 2: 82,978,517 T1727S probably benign Het
Gak A T 5: 108,602,854 S397T probably damaging Het
Gm6040 T A 8: 20,917,097 I36F possibly damaging Het
Grhl1 A G 12: 24,611,861 D513G possibly damaging Het
Gstt1 T A 10: 75,784,106 D219V possibly damaging Het
Hcfc2 T G 10: 82,701,027 V91G probably damaging Het
Hells A T 19: 38,967,783 I808L probably benign Het
Icmt T A 4: 152,299,715 V110E possibly damaging Het
Iqca C T 1: 90,140,038 V164M probably damaging Het
Klri1 G A 6: 129,703,336 P119S probably benign Het
Krt71 C A 15: 101,738,764 probably null Het
Lpin1 A G 12: 16,573,658 probably null Het
Metap2 T C 10: 93,870,197 H241R probably damaging Het
Myh15 A G 16: 49,195,568 Y1869C probably damaging Het
Myo1h G A 5: 114,317,632 G59E possibly damaging Het
Ncam2 T G 16: 81,465,706 probably benign Het
Npat T C 9: 53,555,134 V241A probably benign Het
Npbwr1 C A 1: 5,917,254 V14L probably benign Het
Nup37 T A 10: 88,178,234 V323E possibly damaging Het
Olfr1036 A G 2: 86,075,616 N292S probably damaging Het
Olfr1351 C A 10: 79,017,506 Y61* probably null Het
Olfr483 C T 7: 108,103,591 T94I probably benign Het
Olfr743 A T 14: 50,533,583 Q57L probably benign Het
Ptcd3 T C 6: 71,898,395 D201G probably benign Het
Ptk7 A T 17: 46,586,297 F370I probably benign Het
Pus7l T C 15: 94,533,636 N371D probably benign Het
Pzp G A 6: 128,503,555 A589V probably benign Het
Rasef T A 4: 73,734,549 R572W probably damaging Het
Reep5 T C 18: 34,349,659 T166A probably benign Het
Rhov A G 2: 119,271,020 V35A probably damaging Het
Ripk4 C T 16: 97,743,897 G517R probably damaging Het
Rnasel A G 1: 153,755,054 T439A probably damaging Het
Slamf9 A G 1: 172,477,340 T174A probably benign Het
Slc12a9 A G 5: 137,323,149 L414P probably damaging Het
Slf1 G A 13: 77,066,648 R640* probably null Het
Slfn8 G T 11: 83,016,886 P277Q probably damaging Het
Stpg2 T A 3: 139,419,702 probably benign Het
Tm9sf3 A C 19: 41,223,179 N408K possibly damaging Het
Trio A G 15: 27,758,347 V2049A possibly damaging Het
Ttn A T 2: 76,814,733 I11180N probably damaging Het
Ush2a T C 1: 188,415,821 C982R probably damaging Het
Usp36 C T 11: 118,273,566 V207M probably damaging Het
Uvrag T C 7: 99,118,224 T67A probably damaging Het
Vasp G A 7: 19,260,978 probably benign Het
Vmn2r115 T C 17: 23,359,539 F662S probably damaging Het
Vmn2r54 A T 7: 12,632,507 C167S probably damaging Het
Vmn2r71 C A 7: 85,621,268 N547K probably damaging Het
Wasf2 A G 4: 133,176,591 I37V probably benign Het
Wwc2 T C 8: 47,842,902 E1111G unknown Het
Zfp317 A G 9: 19,647,312 Y274C probably damaging Het
Zhx3 T C 2: 160,781,275 Y324C probably damaging Het
Zzef1 T C 11: 72,864,036 probably null Het
Other mutations in Pdlim4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01377:Pdlim4 APN 11 54,056,304 (GRCm38) missense probably benign 0.43
IGL02005:Pdlim4 APN 11 54,059,984 (GRCm38) missense probably benign 0.10
IGL02305:Pdlim4 APN 11 54,055,933 (GRCm38) missense probably damaging 1.00
IGL03073:Pdlim4 APN 11 54,063,641 (GRCm38) missense probably damaging 1.00
BB001:Pdlim4 UTSW 11 54,055,222 (GRCm38) nonsense probably null
BB011:Pdlim4 UTSW 11 54,055,222 (GRCm38) nonsense probably null
R0008:Pdlim4 UTSW 11 54,055,049 (GRCm38) missense probably damaging 1.00
R0612:Pdlim4 UTSW 11 54,068,887 (GRCm38) missense probably damaging 1.00
R1754:Pdlim4 UTSW 11 54,055,873 (GRCm38) missense possibly damaging 0.82
R2132:Pdlim4 UTSW 11 54,063,737 (GRCm38) missense possibly damaging 0.70
R3037:Pdlim4 UTSW 11 54,056,257 (GRCm38) missense probably benign 0.15
R4210:Pdlim4 UTSW 11 54,055,918 (GRCm38) missense possibly damaging 0.70
R5787:Pdlim4 UTSW 11 54,055,216 (GRCm38) missense probably damaging 1.00
R5969:Pdlim4 UTSW 11 54,063,656 (GRCm38) missense possibly damaging 0.50
R6862:Pdlim4 UTSW 11 54,055,848 (GRCm38) missense probably damaging 1.00
R7924:Pdlim4 UTSW 11 54,055,222 (GRCm38) nonsense probably null
R8927:Pdlim4 UTSW 11 54,059,964 (GRCm38) missense probably benign 0.01
R8928:Pdlim4 UTSW 11 54,059,964 (GRCm38) missense probably benign 0.01
R9023:Pdlim4 UTSW 11 54,068,836 (GRCm38) unclassified probably benign
R9026:Pdlim4 UTSW 11 54,055,454 (GRCm38) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GGAAAGCCAGCATGGTAATTCCAGC -3'
(R):5'- ACCTCAGACTTCCCTTGGAAGGAC -3'

Sequencing Primer
(F):5'- TGAGGCTCTTAGATCAAACGAC -3'
(R):5'- CCCTTCTGACTGTAGAATACGAG -3'
Posted On 2014-04-24