Incidental Mutation 'R6862:Pdlim4'
ID 535710
Institutional Source Beutler Lab
Gene Symbol Pdlim4
Ensembl Gene ENSMUSG00000020388
Gene Name PDZ and LIM domain 4
Synonyms Ril
MMRRC Submission 045026-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.236) question?
Stock # R6862 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 53945754-53959840 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 53946674 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Aspartic acid at position 204 (E204D)
Ref Sequence ENSEMBL: ENSMUSP00000090797 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018755] [ENSMUST00000093109] [ENSMUST00000144477]
AlphaFold P70271
Predicted Effect probably damaging
Transcript: ENSMUST00000018755
AA Change: E204D

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: E204D

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 probably damaging
Transcript: ENSMUST00000093109
AA Change: E204D

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: E204D

DomainStartEndE-ValueType
PDZ 11 84 1.05e-17 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000144477
SMART Domains Protein: ENSMUSP00000121248
Gene: ENSMUSG00000020388

DomainStartEndE-ValueType
Blast:PDZ 1 25 2e-10 BLAST
SCOP:d1qava_ 1 25 3e-4 SMART
PDB:2V1W|B 1 28 2e-11 PDB
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 98.0%
Validation Efficiency 98% (57/58)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579F01Rik C T 3: 137,891,949 (GRCm39) probably benign Het
Adgra2 T A 8: 27,603,465 (GRCm39) C417S probably damaging Het
Adgra2 C A 8: 27,603,464 (GRCm39) H416Q probably benign Het
Aff3 C A 1: 38,445,578 (GRCm39) R307L possibly damaging Het
Arhgap17 T C 7: 122,921,124 (GRCm39) D121G probably damaging Het
Ascc3 G T 10: 50,725,742 (GRCm39) R2155I probably null Het
Ccdc115 C T 1: 34,478,364 (GRCm39) S19N possibly damaging Het
Ccser2 T C 14: 36,662,038 (GRCm39) N382S probably benign Het
Cct6b A T 11: 82,610,785 (GRCm39) V500E probably damaging Het
Cenpo A T 12: 4,266,539 (GRCm39) Y190N probably damaging Het
Cfh T A 1: 140,030,100 (GRCm39) K924N probably damaging Het
Col4a1 A G 8: 11,252,926 (GRCm39) probably benign Het
Coro1b T C 19: 4,200,770 (GRCm39) V234A probably benign Het
Crot T C 5: 9,039,641 (GRCm39) K69E probably damaging Het
Cyp2d11 A T 15: 82,274,339 (GRCm39) H347Q probably benign Het
Efcab3 A T 11: 104,612,284 (GRCm39) K636* probably null Het
Fbn2 T A 18: 58,257,393 (GRCm39) I325F probably benign Het
Fbxw4 T A 19: 45,571,187 (GRCm39) R41S probably benign Het
Fn1 T A 1: 71,653,066 (GRCm39) I1308F probably benign Het
Frem1 C A 4: 82,930,251 (GRCm39) E232* probably null Het
Gabrg3 T C 7: 56,423,059 (GRCm39) Q213R possibly damaging Het
Garin3 G A 11: 46,298,418 (GRCm39) G574D possibly damaging Het
Gsdme A T 6: 50,204,378 (GRCm39) V193E probably damaging Het
Hadha C A 5: 30,352,977 (GRCm39) probably null Het
Hdgfl2 C A 17: 56,406,211 (GRCm39) A533E probably damaging Het
Hivep2 T C 10: 14,006,327 (GRCm39) F975S probably damaging Het
Htatip2 T A 7: 49,420,666 (GRCm39) S171T probably benign Het
Ift57 A T 16: 49,584,167 (GRCm39) I307F possibly damaging Het
Il22 A T 10: 118,041,715 (GRCm39) R110W probably benign Het
Kcnk13 G T 12: 100,027,948 (GRCm39) R341L probably damaging Het
Kif2b G A 11: 91,466,741 (GRCm39) T514M probably damaging Het
Kmt2c A C 5: 25,515,515 (GRCm39) I2776S probably damaging Het
Ly9 T C 1: 171,428,723 (GRCm39) D189G probably benign Het
Mal2 T C 15: 54,451,753 (GRCm39) V58A probably damaging Het
Mettl21e T A 1: 44,245,526 (GRCm39) N240I probably benign Het
Msantd5f1 A G 4: 73,605,621 (GRCm39) N344S probably benign Het
Muc5ac C T 7: 141,363,481 (GRCm39) probably benign Het
Nacc1 G A 8: 85,399,844 (GRCm39) R458C probably damaging Het
Ncapd3 T C 9: 26,942,105 (GRCm39) C14R probably damaging Het
Obscn G T 11: 58,886,279 (GRCm39) probably benign Het
Or13c3 A G 4: 52,855,695 (GRCm39) F273L probably benign Het
Or1j4 A T 2: 36,740,234 (GRCm39) M59L possibly damaging Het
Or8d23 T A 9: 38,841,772 (GRCm39) F102I possibly damaging Het
Parp12 T C 6: 39,088,670 (GRCm39) I189V probably benign Het
Pde4dip C A 3: 97,674,340 (GRCm39) R192L possibly damaging Het
Phf3 T C 1: 30,853,063 (GRCm39) Q1049R probably damaging Het
Prr14l A G 5: 32,985,103 (GRCm39) L1464P probably damaging Het
Psg25 C T 7: 18,255,323 (GRCm39) V398I probably benign Het
Ptprq T A 10: 107,522,086 (GRCm39) N622Y probably damaging Het
Rsf1 CG CGACGGCGGTG 7: 97,229,115 (GRCm39) probably benign Het
Tex36 A G 7: 133,189,002 (GRCm39) L190P probably benign Het
Tk1 A G 11: 117,707,320 (GRCm39) C156R probably damaging Het
Tmem144 T A 3: 79,739,406 (GRCm39) M126L probably benign Het
Tmem208 G A 8: 106,054,862 (GRCm39) probably null Het
Trappc13 T C 13: 104,286,660 (GRCm39) Q199R probably damaging Het
Trim30b T A 7: 104,012,960 (GRCm39) K156N probably damaging Het
Trps1 A G 15: 50,695,001 (GRCm39) probably null Het
Washc4 T A 10: 83,394,757 (GRCm39) F329Y possibly damaging Het
Zbed5 T G 5: 129,932,026 (GRCm39) D658E probably benign Het
Zfyve28 T G 5: 34,445,449 (GRCm39) K11N probably benign Het
Zp1 C T 19: 10,893,877 (GRCm39) V443I possibly damaging Het
Other mutations in Pdlim4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01377:Pdlim4 APN 11 53,947,130 (GRCm39) missense probably benign 0.43
IGL02005:Pdlim4 APN 11 53,950,810 (GRCm39) missense probably benign 0.10
IGL02305:Pdlim4 APN 11 53,946,759 (GRCm39) missense probably damaging 1.00
IGL03073:Pdlim4 APN 11 53,954,467 (GRCm39) missense probably damaging 1.00
BB001:Pdlim4 UTSW 11 53,946,048 (GRCm39) nonsense probably null
BB011:Pdlim4 UTSW 11 53,946,048 (GRCm39) nonsense probably null
R0008:Pdlim4 UTSW 11 53,945,875 (GRCm39) missense probably damaging 1.00
R0612:Pdlim4 UTSW 11 53,959,713 (GRCm39) missense probably damaging 1.00
R1646:Pdlim4 UTSW 11 53,947,080 (GRCm39) missense possibly damaging 0.94
R1754:Pdlim4 UTSW 11 53,946,699 (GRCm39) missense possibly damaging 0.82
R2132:Pdlim4 UTSW 11 53,954,563 (GRCm39) missense possibly damaging 0.70
R3037:Pdlim4 UTSW 11 53,947,083 (GRCm39) missense probably benign 0.15
R4210:Pdlim4 UTSW 11 53,946,744 (GRCm39) missense possibly damaging 0.70
R5787:Pdlim4 UTSW 11 53,946,042 (GRCm39) missense probably damaging 1.00
R5969:Pdlim4 UTSW 11 53,954,482 (GRCm39) missense possibly damaging 0.50
R7924:Pdlim4 UTSW 11 53,946,048 (GRCm39) nonsense probably null
R8927:Pdlim4 UTSW 11 53,950,790 (GRCm39) missense probably benign 0.01
R8928:Pdlim4 UTSW 11 53,950,790 (GRCm39) missense probably benign 0.01
R9023:Pdlim4 UTSW 11 53,959,662 (GRCm39) unclassified probably benign
R9026:Pdlim4 UTSW 11 53,946,280 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GCACAGTCACAGTAAGGCAC -3'
(R):5'- TCGTTTGATCTAAGAGCCTCAAC -3'

Sequencing Primer
(F):5'- TCACAGTAAGGCACAGAGGGATTTG -3'
(R):5'- TTATAGTTTGACTTAGAAGGCTGCC -3'
Posted On 2018-10-18