Incidental Mutation 'R3957:Lmx1b'
ID 310738
Institutional Source Beutler Lab
Gene Symbol Lmx1b
Ensembl Gene ENSMUSG00000038765
Gene Name LIM homeobox transcription factor 1 beta
Synonyms GENA 191, LMX1.2, Icst
MMRRC Submission 040931-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.908) question?
Stock # R3957 (G1)
Quality Score 144
Status Not validated
Chromosome 2
Chromosomal Location 33450977-33530620 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 33459106 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 149 (E149G)
Ref Sequence ENSEMBL: ENSMUSP00000043616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041730]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000041730
AA Change: E149G

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000043616
Gene: ENSMUSG00000038765
AA Change: E149G

DomainStartEndE-ValueType
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: ENSMUST00000137559
SMART Domains Protein: ENSMUSP00000115288
Gene: ENSMUSG00000038765

DomainStartEndE-ValueType
LIM 9 63 5.51e-17 SMART
low complexity region 69 90 N/A INTRINSIC
low complexity region 95 118 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000176067
AA Change: E138G
SMART Domains Protein: ENSMUSP00000134944
Gene: ENSMUSG00000038765
AA Change: E138G

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.9%
  • 20x: 93.5%
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 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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330159F19Rik A G 10: 29,100,805 (GRCm39) K393E possibly damaging Het
Acsm4 A T 7: 119,302,588 (GRCm39) M238L possibly damaging Het
Adam2 G A 14: 66,295,059 (GRCm39) S262L probably damaging Het
Atp13a5 T A 16: 29,117,012 (GRCm39) I579L probably benign Het
Canx A G 11: 50,199,210 (GRCm39) V153A probably damaging Het
Cdan1 A G 2: 120,556,113 (GRCm39) Y718H probably damaging Het
Cdan1 G A 2: 120,561,501 (GRCm39) probably benign Het
Cpsf3 A G 12: 21,363,806 (GRCm39) D632G probably benign Het
Dach1 T C 14: 98,077,545 (GRCm39) T561A probably damaging Het
Dennd5a A G 7: 109,504,906 (GRCm39) M868T probably benign Het
Dhx29 C T 13: 113,067,455 (GRCm39) A112V probably benign Het
Fanca G A 8: 124,043,102 (GRCm39) R95C probably benign Het
Fat4 C A 3: 39,036,495 (GRCm39) N3382K probably benign Het
Fkbp15 A C 4: 62,252,489 (GRCm39) F290L probably benign Het
Fkbp8 T G 8: 70,987,517 (GRCm39) S376A probably damaging Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Igfn1 A G 1: 135,894,918 (GRCm39) Y1883H possibly damaging Het
Ighv3-4 T A 12: 114,217,300 (GRCm39) Q97L probably damaging Het
Igkv15-103 A T 6: 68,414,903 (GRCm39) Y114F probably benign Het
Kera G A 10: 97,448,707 (GRCm39) R309H probably benign Het
Kif1a T A 1: 92,953,416 (GRCm39) H1256L probably damaging Het
Kremen1 CGGG CGGGGGG 11: 5,151,791 (GRCm39) probably benign Het
Me2 A G 18: 73,914,203 (GRCm39) F443L probably damaging Het
Med12l T A 3: 58,980,589 (GRCm39) S307R probably damaging Het
Mettl25b T C 3: 87,834,135 (GRCm39) K116R possibly damaging Het
Mocs2 T A 13: 114,961,803 (GRCm39) probably null Het
Nek7 C A 1: 138,462,127 (GRCm39) C79F probably damaging Het
Or14j6 A T 17: 38,214,500 (GRCm39) H21L probably benign Het
Or51f1 A G 7: 102,505,824 (GRCm39) C222R probably damaging Het
Or5al1 A G 2: 85,990,282 (GRCm39) V144A probably benign Het
Or5d43 A G 2: 88,105,348 (GRCm39) F15S probably damaging Het
Ovch2 G A 7: 107,388,318 (GRCm39) L421F probably damaging Het
Pan2 C T 10: 128,151,046 (GRCm39) R806C probably damaging Het
Plod3 A T 5: 137,023,046 (GRCm39) H616L probably damaging Het
Plxnb3 T C X: 72,814,826 (GRCm39) V1789A probably benign Het
Ptgir A G 7: 16,640,794 (GRCm39) M29V possibly damaging Het
Tbc1d9 C T 8: 83,960,161 (GRCm39) T138I probably damaging Het
Tdrkh A G 3: 94,335,556 (GRCm39) N383S probably damaging Het
Trim30d C T 7: 104,121,728 (GRCm39) G339D probably damaging Het
Trub1 G A 19: 57,473,798 (GRCm39) A239T possibly damaging Het
Tspan32 T A 7: 142,560,735 (GRCm39) M61K probably damaging Het
Ttc6 T C 12: 57,744,238 (GRCm39) V1290A probably benign Het
Ttn A G 2: 76,799,593 (GRCm39) V429A possibly damaging Het
Unc13b A G 4: 43,256,834 (GRCm39) Y3962C probably damaging Het
Usp3 T C 9: 66,469,873 (GRCm39) T83A probably benign Het
Vmn2r95 T A 17: 18,660,358 (GRCm39) Y257N possibly damaging Het
Zmym6 T C 4: 127,017,089 (GRCm39) S957P possibly damaging Het
Zmynd8 T C 2: 165,654,395 (GRCm39) T722A probably damaging 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
R3522:Lmx1b UTSW 2 33,529,543 (GRCm39) missense probably benign 0.01
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
(F):5'- TGTGACACCTTGATGCTGGC -3'
(R):5'- TAGAGCTGACCACCCAAGAG -3'

Sequencing Primer
(F):5'- CTGGCCATGCACGGACATG -3'
(R):5'- TCTTCGCGGCAAAGTGC -3'
Posted On 2015-04-29