Incidental Mutation 'R4210:Pdlim4'
ID 319144
Institutional Source Beutler Lab
Gene Symbol Pdlim4
Ensembl Gene ENSMUSG00000020388
Gene Name PDZ and LIM domain 4
Synonyms Ril
MMRRC Submission 041039-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.236) question?
Stock # R4210 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 53945754-53959840 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 53946744 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Alanine at position 181 (D181A)
Ref Sequence ENSEMBL: ENSMUSP00000090797 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018755] [ENSMUST00000093109] [ENSMUST00000144477]
AlphaFold P70271
Predicted Effect probably benign
Transcript: ENSMUST00000018755
AA Change: D181A

PolyPhen 2 Score 0.222 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000018755
Gene: ENSMUSG00000020388
AA Change: D181A

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: D181A

PolyPhen 2 Score 0.696 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000090797
Gene: ENSMUSG00000020388
AA Change: D181A

DomainStartEndE-ValueType
PDZ 11 84 1.05e-17 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127271
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: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 95.0%
Validation Efficiency
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik C T 2: 68,490,222 (GRCm39) probably benign Het
Abl1 T C 2: 31,691,708 (GRCm39) Y1076H probably damaging Het
Adamts7 C T 9: 90,076,063 (GRCm39) T1265I possibly damaging Het
Adgb T C 10: 10,283,209 (GRCm39) I166V probably benign Het
Axin2 T A 11: 108,833,402 (GRCm39) I529N possibly damaging Het
Bbof1 T C 12: 84,455,957 (GRCm39) M1T probably null Het
Clcc1 A T 3: 108,570,907 (GRCm39) Y105F possibly damaging Het
Cmpk2 G T 12: 26,519,570 (GRCm39) A74S probably benign Het
Colgalt1 G A 8: 72,075,350 (GRCm39) V419I probably benign Het
Crybg3 A G 16: 59,364,414 (GRCm39) S2403P probably damaging Het
D930048N14Rik G A 11: 51,545,632 (GRCm39) probably benign Het
Dnah7b T A 1: 46,176,578 (GRCm39) C733S possibly damaging Het
Drc1 G A 5: 30,504,490 (GRCm39) V211M possibly damaging Het
Ephx2 T C 14: 66,322,393 (GRCm39) T525A probably damaging Het
Eya4 A G 10: 23,102,698 (GRCm39) probably null Het
Foxc1 T C 13: 31,991,690 (GRCm39) F167S probably damaging Het
Fsip2 C T 2: 82,805,493 (GRCm39) T604I probably damaging Het
Gm6370 C A 5: 146,430,734 (GRCm39) F306L possibly damaging Het
Hmgcr A G 13: 96,796,729 (GRCm39) V187A probably damaging Het
Igkv9-129 T A 6: 67,817,242 (GRCm39) S114R possibly damaging Het
Ikbke T A 1: 131,191,085 (GRCm39) I519F probably damaging Het
Ikzf3 T C 11: 98,381,313 (GRCm39) Y89C probably benign Het
Inpp5j T G 11: 3,451,107 (GRCm39) H514P probably damaging Het
Iqsec3 T C 6: 121,389,999 (GRCm39) probably benign Het
Itga3 C A 11: 94,953,449 (GRCm39) V298L probably benign Het
Kel C T 6: 41,675,359 (GRCm39) W297* probably null Het
Larp7 T A 3: 127,340,603 (GRCm39) R112S probably benign Het
Lbh T A 17: 73,228,178 (GRCm39) probably null Het
Lrba G A 3: 86,267,433 (GRCm39) G1708S probably damaging Het
Lrig2 C T 3: 104,374,620 (GRCm39) V154I probably benign Het
Man1c1 G C 4: 134,430,749 (GRCm39) P11R probably damaging Het
Mast4 A T 13: 102,875,713 (GRCm39) F1318L probably damaging Het
Ncam2 T C 16: 81,323,991 (GRCm39) V545A probably benign Het
Numa1 T G 7: 101,658,945 (GRCm39) L356R probably damaging Het
Or2w1 A T 13: 21,317,607 (GRCm39) I221L possibly damaging Het
Or6n2 G A 1: 173,897,574 (GRCm39) A237T probably damaging Het
Pcgf5 C A 19: 36,414,740 (GRCm39) N26K possibly damaging Het
Phtf1 G A 3: 103,910,919 (GRCm39) probably null Het
Pik3r4 G A 9: 105,527,957 (GRCm39) A437T possibly damaging Het
Proser3 G A 7: 30,245,525 (GRCm39) probably benign Het
Rax T A 18: 66,068,152 (GRCm39) N318Y unknown Het
Rnf152 A G 1: 105,212,077 (GRCm39) V160A probably benign Het
Serpina3a A T 12: 104,084,902 (GRCm39) D99V probably benign Het
Sidt2 T C 9: 45,854,073 (GRCm39) T652A probably benign Het
Slc12a7 A G 13: 73,962,962 (GRCm39) Y1054C probably damaging Het
Slc9a5 A G 8: 106,085,103 (GRCm39) N535D possibly damaging Het
Sspo C A 6: 48,441,835 (GRCm39) H1948Q probably benign Het
Stap2 G T 17: 56,304,827 (GRCm39) Y318* probably null Het
Sytl1 T C 4: 132,980,876 (GRCm39) D421G probably damaging Het
Taar7e A T 10: 23,913,932 (GRCm39) I141F probably damaging Het
Taar7f T A 10: 23,925,921 (GRCm39) W172R probably damaging Het
Tcn2 T C 11: 3,872,114 (GRCm39) K338E possibly damaging Het
Tenm3 C T 8: 48,802,439 (GRCm39) G374D probably damaging Het
Terf2 A G 8: 107,806,080 (GRCm39) S291P probably damaging Het
Tex16 T A X: 111,030,640 (GRCm39) D1046E probably benign Het
Tmod4 A G 3: 95,035,140 (GRCm39) D215G probably benign Het
Tnxb T C 17: 34,929,951 (GRCm39) I2895T possibly damaging Het
Tsbp1 G T 17: 34,679,257 (GRCm39) probably benign Het
Urgcp C A 11: 5,665,878 (GRCm39) G820V probably damaging Het
Uxs1 T A 1: 43,789,398 (GRCm39) H419L possibly damaging Het
Vmn1r152 A T 7: 22,223,004 (GRCm39) T205S possibly damaging Het
Vmn1r79 A G 7: 11,910,415 (GRCm39) Y99C possibly damaging Het
Zc3h14 A G 12: 98,751,658 (GRCm39) H199R probably damaging Het
Zfand2b A T 1: 75,146,454 (GRCm39) M110L probably benign Het
Zfp976 A G 7: 42,265,749 (GRCm39) F12S probably 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
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
R6862:Pdlim4 UTSW 11 53,946,674 (GRCm39) missense probably damaging 1.00
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'- GCCTTTGAAGTCACACCCAG -3'

Sequencing Primer
(F):5'- TCACAGTAAGGCACAGAGGGATTTG -3'
(R):5'- TTTGAAGTCACACCCAGATCAATC -3'
Posted On 2015-06-10