Incidental Mutation 'R3522:Lmx1b'
ID 267508
Institutional Source Beutler Lab
Gene Symbol Lmx1b
Ensembl Gene ENSMUSG00000038765
Gene Name LIM homeobox transcription factor 1 beta
Synonyms GENA 191, LMX1.2, Icst
Accession Numbers
Essential gene? Probably essential (E-score: 0.906) question?
Stock # R3522 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 33450977-33530620 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 33529543 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Phenylalanine at position 72 (Y72F)
Ref Sequence ENSEMBL: ENSMUSP00000043616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041730]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000041730
AA Change: Y72F

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000043616
Gene: ENSMUSG00000038765
AA Change: Y72F

LIM 32 83 4.48e-17 SMART
LIM 91 145 5.51e-17 SMART
low complexity region 151 172 N/A INTRINSIC
HOX 196 258 1.51e-21 SMART
low complexity region 259 272 N/A INTRINSIC
low complexity region 328 340 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147294
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152118
Predicted Effect unknown
Transcript: ENSMUST00000176067
AA Change: Y61F
SMART Domains Protein: ENSMUSP00000134944
Gene: ENSMUSG00000038765
AA Change: Y61F

LIM 1 38 2.23e-3 SMART
LIM 46 100 5.51e-17 SMART
low complexity region 106 127 N/A INTRINSIC
HOX 151 213 1.51e-21 SMART
low complexity region 214 227 N/A INTRINSIC
low complexity region 290 302 N/A INTRINSIC
Meta Mutation Damage Score 0.0929 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.8%
Validation Efficiency 100% (72/72)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit various skeletal, kidney, and eye defects. Pups also fail to suckle. Heterozygous mice with a homeodomain V265D mutation exhibit a variety of eye defects. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ankrd35 A G 3: 96,592,378 (GRCm39) E888G probably damaging Het
Arhgef10 T C 8: 15,004,918 (GRCm39) F150S probably damaging Het
Atp10d G T 5: 72,396,500 (GRCm39) R235L probably benign Het
Cacna1b A G 2: 24,653,055 (GRCm39) V2A possibly damaging Het
Cand1 A T 10: 119,075,102 (GRCm39) L15Q probably benign Het
Cavin3 C A 7: 105,130,350 (GRCm39) G154V probably benign Het
Ccdc73 A T 2: 104,821,830 (GRCm39) D593V probably damaging Het
Cdk5rap2 T C 4: 70,168,647 (GRCm39) K161E probably damaging Het
Chil4 A T 3: 106,111,056 (GRCm39) N279K probably benign Het
Chst13 T G 6: 90,295,245 (GRCm39) D56A probably damaging Het
Cnn1 C A 9: 22,010,664 (GRCm39) H5N probably benign Het
Cpsf4l T A 11: 113,593,319 (GRCm39) K88N probably damaging Het
Ctnnbl1 G T 2: 157,713,113 (GRCm39) probably null Het
Dnah7a A C 1: 53,657,275 (GRCm39) F834V probably damaging Het
Fbxo41 A G 6: 85,461,163 (GRCm39) S182P probably benign Het
Fkbp5 T C 17: 28,634,970 (GRCm39) T180A probably benign Het
Flg2 T A 3: 93,127,334 (GRCm39) I2082N unknown Het
Gm4968 A G 6: 127,210,725 (GRCm39) noncoding transcript Het
Gpc5 T A 14: 116,761,747 (GRCm39) H612Q probably benign Het
Gsg1 A T 6: 135,218,251 (GRCm39) V212D probably damaging Het
Hipk1 A G 3: 103,651,430 (GRCm39) V1111A probably damaging Het
Hormad1 A T 3: 95,483,596 (GRCm39) Q136L probably benign Het
Ifi35 T A 11: 101,348,511 (GRCm39) S147R probably benign Het
Iqca1l A G 5: 24,754,624 (GRCm39) probably null Het
Iqgap3 C T 3: 87,998,089 (GRCm39) A282V probably null Het
Jmy T C 13: 93,590,558 (GRCm39) D515G probably damaging Het
Kctd10 G A 5: 114,512,984 (GRCm39) R64C probably damaging Het
Kidins220 T C 12: 25,040,757 (GRCm39) V121A probably damaging Het
Lcn3 G A 2: 25,656,133 (GRCm39) V63M possibly damaging Het
Lrp1 T C 10: 127,389,424 (GRCm39) D3164G probably damaging Het
Mdh1b C T 1: 63,758,927 (GRCm39) V222M probably damaging Het
Mst1 T C 9: 107,958,702 (GRCm39) probably benign Het
Myo7b C A 18: 32,143,132 (GRCm39) V189F probably damaging Het
Ndc1 T C 4: 107,250,355 (GRCm39) S533P probably damaging Het
Ndrg3 T C 2: 156,785,947 (GRCm39) D164G probably damaging Het
Nol11 C T 11: 107,064,454 (GRCm39) C500Y possibly damaging Het
Nsd3 A G 8: 26,196,642 (GRCm39) N1208D probably benign Het
Nup155 C T 15: 8,186,162 (GRCm39) probably benign Het
Or5ak20 A T 2: 85,183,347 (GRCm39) C308S probably benign Het
Or6c38 A G 10: 128,929,711 (GRCm39) I44T possibly damaging Het
Or8b47 A G 9: 38,435,081 (GRCm39) T18A probably damaging Het
Or8b54 A T 9: 38,687,016 (GRCm39) D155V possibly damaging Het
Phf3 A G 1: 30,844,684 (GRCm39) L1425P probably damaging Het
Pla2r1 A G 2: 60,279,250 (GRCm39) Y777H probably damaging Het
Pld1 A G 3: 28,085,396 (GRCm39) E184G probably damaging Het
Plxna1 T C 6: 89,314,335 (GRCm39) probably null Het
Ptgfrn T C 3: 100,950,718 (GRCm39) E865G probably damaging Het
Ptpn13 G T 5: 103,737,720 (GRCm39) probably benign Het
Pygb G T 2: 150,670,473 (GRCm39) V763F probably benign Het
Ros1 A C 10: 51,967,091 (GRCm39) Y1705* probably null Het
Sec61a2 A G 2: 5,898,027 (GRCm39) F5L probably benign Het
Skint5 A G 4: 113,614,102 (GRCm39) probably null Het
Sntg2 A G 12: 30,362,566 (GRCm39) V60A probably damaging Het
Sppl2a A G 2: 126,762,242 (GRCm39) C280R possibly damaging Het
Srrm4 A C 5: 116,584,603 (GRCm39) M1R probably null Het
Sult1c2 T C 17: 54,279,043 (GRCm39) E91G probably damaging Het
Themis2 C G 4: 132,512,906 (GRCm39) R440P probably damaging Het
Tmem229a A G 6: 24,955,058 (GRCm39) L232P probably benign Het
Trappc1 T C 11: 69,215,248 (GRCm39) F43L probably damaging Het
Trappc11 A T 8: 47,951,708 (GRCm39) Y982N possibly damaging Het
Trpv6 A T 6: 41,604,339 (GRCm39) M139K probably damaging Het
Txnrd3 A G 6: 89,640,057 (GRCm39) probably null Het
Vmn1r184 T A 7: 25,967,008 (GRCm39) Y251* probably null Het
Vmn1r216 A G 13: 23,283,544 (GRCm39) N76D possibly damaging Het
Vmn1r71 C A 7: 10,481,792 (GRCm39) V233F probably benign Het
Vps13a A C 19: 16,743,857 (GRCm39) probably benign Het
Vwa5b2 A G 16: 20,420,358 (GRCm39) S756G probably damaging Het
Wdr36 T A 18: 32,994,538 (GRCm39) probably null Het
Wdr86 A G 5: 24,923,305 (GRCm39) V129A probably benign Het
Zfyve9 A G 4: 108,576,940 (GRCm39) L47S probably benign Het
Other mutations in Lmx1b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01539:Lmx1b APN 2 33,529,510 (GRCm39) missense possibly damaging 0.95
IGL01583:Lmx1b APN 2 33,459,071 (GRCm39) missense probably benign 0.04
IGL02885:Lmx1b APN 2 33,457,216 (GRCm39) missense probably benign 0.10
R1926:Lmx1b UTSW 2 33,454,674 (GRCm39) missense probably damaging 1.00
R3056:Lmx1b UTSW 2 33,457,297 (GRCm39) nonsense probably null
R3957:Lmx1b UTSW 2 33,459,106 (GRCm39) missense probably damaging 0.99
R4888:Lmx1b UTSW 2 33,454,802 (GRCm39) missense probably benign 0.01
R6115:Lmx1b UTSW 2 33,459,118 (GRCm39) missense probably damaging 0.96
R8254:Lmx1b UTSW 2 33,455,126 (GRCm39) missense
R8787:Lmx1b UTSW 2 33,529,522 (GRCm39) missense
RF032:Lmx1b UTSW 2 33,530,501 (GRCm39) nonsense probably null
RF035:Lmx1b UTSW 2 33,530,501 (GRCm39) nonsense probably null
RF038:Lmx1b UTSW 2 33,530,521 (GRCm39) start codon destroyed probably null
RF043:Lmx1b UTSW 2 33,530,521 (GRCm39) start codon destroyed probably null
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2015-02-18