Incidental Mutation 'R4211:Lmx1a'
ID 319172
Institutional Source Beutler Lab
Gene Symbol Lmx1a
Ensembl Gene ENSMUSG00000026686
Gene Name LIM homeobox transcription factor 1 alpha
Synonyms shaker short-tail, Lmx1.1
Accession Numbers
Essential gene? Probably essential (E-score: 0.883) question?
Stock # R4211 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 167516806-167676310 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 167660428 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 238 (V238L)
Ref Sequence ENSEMBL: ENSMUSP00000107008 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028003] [ENSMUST00000111377]
AlphaFold Q9JKU8
Predicted Effect probably damaging
Transcript: ENSMUST00000028003
AA Change: V238L

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: V238L

DomainStartEndE-ValueType
LIM 34 85 2.87e-15 SMART
LIM 93 147 3.39e-17 SMART
HOX 195 257 2.62e-21 SMART
low complexity region 337 350 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000111377
AA Change: V238L

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: V238L

DomainStartEndE-ValueType
LIM 34 85 2.87e-15 SMART
LIM 93 147 3.39e-17 SMART
HOX 195 257 2.62e-21 SMART
low complexity region 337 350 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
PHENOTYPE: Mutations in the dreher locus produce neurological and skeletal abnormalities, inner ear defects, and belly spotting. Deafness and hypoplasia of Mullerian duct derivatives are also reported for some alleles. Homozygous null mice have fewer dopaminergic neurons. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgb T C 10: 10,283,209 (GRCm39) I166V probably benign Het
Albfm1 T G 5: 90,712,096 (GRCm39) V63G probably damaging Het
Anapc5 T C 5: 122,955,968 (GRCm39) E154G probably benign Het
Anpep A T 7: 79,490,744 (GRCm39) Y257* probably null Het
Atp8b1 A T 18: 64,686,118 (GRCm39) D688E probably damaging Het
Bub1b C A 2: 118,461,459 (GRCm39) H670Q possibly damaging Het
Casp3 G T 8: 47,088,423 (GRCm39) D107Y probably damaging Het
Castor2 T C 5: 134,154,783 (GRCm39) probably null Het
Clcc1 A T 3: 108,570,907 (GRCm39) Y105F possibly damaging Het
Cr2 A C 1: 194,838,636 (GRCm39) L671R probably damaging Het
Cttnbp2 A G 6: 18,427,542 (GRCm39) V713A probably damaging Het
Cyp4a31 T C 4: 115,422,210 (GRCm39) F65L probably benign Het
Dpysl2 T C 14: 67,052,926 (GRCm39) S308G probably damaging Het
Dusp22 A T 13: 30,892,726 (GRCm39) I168F probably benign Het
Ecel1 A G 1: 87,079,872 (GRCm39) S414P probably damaging Het
Fat2 A G 11: 55,174,810 (GRCm39) F1968L probably damaging Het
Fsip2 C T 2: 82,805,493 (GRCm39) T604I probably damaging Het
H2-DMb1 T A 17: 34,374,547 (GRCm39) F66I possibly damaging Het
Hgf T C 5: 16,819,991 (GRCm39) V574A probably damaging Het
Hoxa7 A T 6: 52,193,605 (GRCm39) Y137* probably null Het
Ikbke T A 1: 131,191,085 (GRCm39) I519F probably damaging Het
Inpp5j T G 11: 3,451,107 (GRCm39) H514P probably damaging Het
Kmt2d A G 15: 98,738,070 (GRCm39) probably benign Het
Larp7 T A 3: 127,340,603 (GRCm39) R112S probably benign Het
Lepr C T 4: 101,590,611 (GRCm39) A63V probably benign Het
Man1c1 G C 4: 134,430,749 (GRCm39) P11R probably damaging Het
Mcmbp T C 7: 128,317,729 (GRCm39) E172G possibly damaging Het
Mcpt8 G A 14: 56,321,375 (GRCm39) H30Y probably damaging Het
Nek8 C A 11: 78,061,309 (GRCm39) V379L probably benign Het
Numa1 T G 7: 101,658,945 (GRCm39) L356R probably damaging Het
Pard6b C T 2: 167,940,943 (GRCm39) A310V probably benign Het
Pcgf5 C A 19: 36,414,740 (GRCm39) N26K possibly damaging Het
Phtf1 G A 3: 103,910,919 (GRCm39) probably null Het
Plch1 C A 3: 63,618,640 (GRCm39) D675Y probably damaging Het
Plk2 A G 13: 110,532,871 (GRCm39) H144R probably damaging Het
Rax T A 18: 66,068,152 (GRCm39) N318Y unknown Het
Slc9a5 A G 8: 106,085,103 (GRCm39) N535D possibly damaging Het
Smarcd2 T A 11: 106,157,731 (GRCm39) K138* probably null 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
Tango6 A G 8: 107,415,856 (GRCm39) I226V probably benign Het
Tcn2 T C 11: 3,872,114 (GRCm39) K338E possibly damaging Het
Tdp1 C A 12: 99,864,588 (GRCm39) A243E probably damaging Het
Tfpt A G 7: 3,623,386 (GRCm39) Y240H probably damaging Het
Tmod4 A G 3: 95,035,140 (GRCm39) D215G probably benign Het
Top3b A G 16: 16,700,396 (GRCm39) probably null Het
Urgcp C A 11: 5,665,878 (GRCm39) G820V probably damaging Het
Zfand2b A T 1: 75,146,454 (GRCm39) M110L probably benign Het
Zfyve1 A T 12: 83,621,909 (GRCm39) V162E probably damaging Het
Other mutations in Lmx1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02624:Lmx1a APN 1 167,672,192 (GRCm39) splice site probably benign
IGL02629:Lmx1a APN 1 167,672,192 (GRCm39) splice site probably benign
IGL02637:Lmx1a APN 1 167,672,192 (GRCm39) splice site probably benign
IGL02642:Lmx1a APN 1 167,672,192 (GRCm39) splice site probably benign
IGL02811:Lmx1a APN 1 167,618,943 (GRCm39) missense probably benign 0.06
scooby UTSW 1 167,658,256 (GRCm39) missense possibly damaging 0.47
R0320:Lmx1a UTSW 1 167,618,973 (GRCm39) nonsense probably null
R1217:Lmx1a UTSW 1 167,618,968 (GRCm39) missense probably damaging 1.00
R2897:Lmx1a UTSW 1 167,658,109 (GRCm39) splice site probably benign
R4976:Lmx1a UTSW 1 167,619,123 (GRCm39) missense possibly damaging 0.73
R5125:Lmx1a UTSW 1 167,658,256 (GRCm39) missense possibly damaging 0.47
R6858:Lmx1a UTSW 1 167,660,450 (GRCm39) missense probably damaging 1.00
R7099:Lmx1a UTSW 1 167,658,115 (GRCm39) missense probably damaging 1.00
R7177:Lmx1a UTSW 1 167,674,247 (GRCm39) missense probably benign
R7380:Lmx1a UTSW 1 167,519,609 (GRCm39) missense probably damaging 1.00
R7831:Lmx1a UTSW 1 167,668,521 (GRCm39) missense probably benign 0.06
R8329:Lmx1a UTSW 1 167,517,372 (GRCm39) missense probably benign 0.00
R9269:Lmx1a UTSW 1 167,658,194 (GRCm39) missense probably benign 0.03
Z1176:Lmx1a UTSW 1 167,519,568 (GRCm39) missense possibly damaging 0.86
Predicted Primers PCR Primer
(F):5'- TTAGGAATGTGACCTATGCCCC -3'
(R):5'- ACACAGACACTTCGCTTCTC -3'

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