Incidental Mutation 'RF038:Lmx1b'
ID 604651
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 # RF038 (G1)
Quality Score 217.468
Status Not validated
Chromosome 2
Chromosomal Location 33450977-33530620 bp(-) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) CATCTTGATGCCGTCCAA to C at 33530521 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000043616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041730]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000041730
SMART Domains Protein: ENSMUSP00000043616
Gene: ENSMUSG00000038765

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 probably benign
Transcript: ENSMUST00000176067
SMART Domains Protein: ENSMUSP00000134944
Gene: ENSMUSG00000038765

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: 99.8%
  • 3x: 99.7%
  • 10x: 99.3%
  • 20x: 98.5%
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A030005L19Rik TGT TGTAGCTGCGGT 1: 82,891,301 (GRCm39) probably benign Het
Abcf1 CTCTTC CTC 17: 36,274,093 (GRCm39) probably benign Het
Acap3 GCATCCTGGGCTGCT GCATCCTGGGCTGCTTCATCCTGGGCTGCT 4: 155,989,549 (GRCm39) probably benign Het
AI837181 GGC GGCAGC 19: 5,475,254 (GRCm39) probably benign Het
AI837181 GCG GCGACG 19: 5,475,264 (GRCm39) probably benign Het
Cdx1 CTGCTG CTGCTGGTGCTG 18: 61,152,942 (GRCm39) probably benign Het
Cyb5r4 CCAGGGA CCAGGGATGTGACACACACACTGCGCAGGGA 9: 86,922,495 (GRCm39) probably benign Het
Dbr1 GAGGAG GAGGAGAAGGAG 9: 99,465,750 (GRCm39) probably benign Het
Dennd10 ACTC ACTCCTC 19: 60,803,056 (GRCm39) probably benign Het
Dmkn GTGGAAGTGGTGG GTGGAAGTGGTGGAAGTGGTGGAAGTGTTGGAAGTGGTGG 7: 30,466,619 (GRCm39) probably benign Het
Dnaaf9 CTC CTCATC 2: 130,612,664 (GRCm39) probably null Het
Enah TGGCGGCGG TGG 1: 181,749,500 (GRCm39) probably benign Het
Flywch1 ACCCACTCCTGGTGT ACCCACTCCTGGTGTGGGGAGGCTACGTACTCCCCCACTCCTGGTGT 17: 23,981,138 (GRCm39) probably null Het
Foxd3 GGACCCTACGGCCG GG 4: 99,545,633 (GRCm39) probably benign Het
Fscb CTTCTACAGGGGCCTCCTCAGTTGCTGGAGGTAGAACTTCTACAGGGGCCTCCTCAGTTGCTGGAGGT CTTCTACAGGGGCCTCCTCAGTTGCTGGAGGTAGAAATTCTACAGGGGCCTCCTCAGTTGCTGGAGGTAGAACTTCTACAGGGGCCTCCTCAGTTGCTGGAGGT 12: 64,519,343 (GRCm39) probably benign Het
Fsip2 TAGATGTGAAACCCTTAGAGGTAAGATGTGAAACTCTTAGAGGTAAGA TAGATGTGAAACTCTTAGAGGTAAGA 2: 82,824,352 (GRCm39) probably null Het
Garin5a TGGGTCTGAGGGAGGA TGGGTCTGAGGGAGGAAGGCTGGATCCTGGATACCGGGGTCTGAGGGAGGA 7: 44,149,946 (GRCm39) probably null Het
Gas1 AG AGATG 13: 60,324,344 (GRCm39) probably benign Het
Gas1 CGAGGA CGAGGAGGA 13: 60,324,342 (GRCm39) probably benign Het
Gm15155 CAAAAA CAAAAACAAAAAA X: 155,128,636 (GRCm39) probably null Het
Habp4 TGAGG TG 13: 64,309,976 (GRCm39) probably benign Het
Hsdl2 CACAGCTGCAG CACAGCTGCAGCAGCAGCGACAGCTGCAG 4: 59,610,648 (GRCm39) probably benign Het
Il2 CTT CTTCAAGTGGGGATT 3: 37,179,970 (GRCm39) probably null Het
Irag2 TG TGAGCACATCG 6: 145,119,516 (GRCm39) probably benign Het
Ivl CTTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 3: 92,479,607 (GRCm39) probably benign Het
Krtap28-10 CA CAACCAAA 1: 83,019,849 (GRCm39) probably benign Het
Krtap28-10 CAGCCACAGCCACCACAGCCACAGCCACCA CAGCCACAGCCACCAAAGCCACAGCCACCACAGCCACAGCCACCA 1: 83,019,978 (GRCm39) probably benign Het
Mamld1 CAG CAGGAG X: 70,162,452 (GRCm39) probably benign Het
Nefh CTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC CTGGGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC 11: 4,891,027 (GRCm39) probably benign Het
Nefh GGGGACTTGGCCTCACCTGGGGACTTGGCCTC GGGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC 11: 4,891,029 (GRCm39) probably benign Het
Nefh CTCACCTGGGGACTTGGC CTCACCTGGGGACTTGGCATCACCTGGGGACTTGGC 11: 4,891,040 (GRCm39) probably benign Het
Nefh GGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC GGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC 11: 4,891,012 (GRCm39) probably benign Het
Nefh TGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC TGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC 11: 4,891,018 (GRCm39) probably benign Het
Nefh GGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC GGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTCACCTGGGGACTTGGCCTC 11: 4,891,019 (GRCm39) probably benign Het
Pabpc6 AGCTGC AGC 17: 9,887,044 (GRCm39) probably benign Het
Pkhd1l1 TTTTTT TTTTTTTTGTTTTT 15: 44,421,899 (GRCm39) probably benign Het
Rassf6 TGTAGAGCAATGGGGATTC TGTAGAGCAATGGGGATTCTGCCTCACTCATGGTCCAGTAGAGCAATGGGGATTC 5: 90,756,783 (GRCm39) probably benign Het
Rassf6 GCAATGGGGATTC GCAATGGGGATTCTGCCTCACTCATGGTCCTGTAGATCAATGGGGATTC 5: 90,756,789 (GRCm39) probably benign Het
Rbm12 CAGGTATTGCGGGACC CAGGTATTGCGGGACCTGGTATTGCGGGACCAGGTATTGCGGGACC 2: 155,938,026 (GRCm39) probably benign Het
Sbp AAGATG AAGATGCTGACAACACAGATG 17: 24,164,358 (GRCm39) probably benign Het
Strn CCCAGTC CCCAGTCCGTGCTCCCTTACCCCAGTCCGTGCTCCCTTACGCCAGTC 17: 78,984,711 (GRCm39) probably null Het
Supt20 TTCAGCA TTCAGCATCAGCA 3: 54,635,068 (GRCm39) probably benign Het
Tcof1 TCCCAGAGATCCCC TCCCAGAGATCCCCCTGGCTGCTGAGATGGGCACTTCCCCAGAGATCCCC 18: 60,966,638 (GRCm39) probably benign Het
Tfeb AGC AGCGGC 17: 48,097,030 (GRCm39) probably benign Het
Tfeb GCA GCACCA 17: 48,097,037 (GRCm39) probably benign Het
Trappc9 GCTGCTGCT GCTGCTGCTGCTGCTCCTGCTGCT 15: 72,673,172 (GRCm39) probably benign Het
Zfhx3 CAGCA CAGCACCAGAAGCA 8: 109,682,733 (GRCm39) 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
R3522:Lmx1b UTSW 2 33,529,543 (GRCm39) missense probably benign 0.01
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
RF043:Lmx1b UTSW 2 33,530,521 (GRCm39) start codon destroyed probably null
Predicted Primers PCR Primer
(F):5'- GTGACGTCCCTGAACGTTTTCC -3'
(R):5'- CTGACAAGCAGGTGACAGGC -3'

Sequencing Primer
(F):5'- TGGTCATTCCAGGGGTCC -3'
(R):5'- CGAGTAGCCGGTAGAGAGC -3'
Posted On 2019-12-04