Incidental Mutation 'R1217:Lmx1a'
ID 99713
Institutional Source Beutler Lab
Gene Symbol Lmx1a
Ensembl Gene ENSMUSG00000026686
Gene Name LIM homeobox transcription factor 1 alpha
Synonyms shaker short-tail, Lmx1.1
MMRRC Submission 039286-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.883) question?
Stock # R1217 (G1)
Quality Score 124
Status Validated
Chromosome 1
Chromosomal Location 167516806-167676310 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 167618968 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 109 (R109H)
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: R109H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: R109H

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: R109H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: R109H

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
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.8%
  • 20x: 87.6%
Validation Efficiency 100% (45/45)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adora2a A T 10: 75,169,049 (GRCm39) Y171F probably damaging Het
Agpat4 C T 17: 12,429,203 (GRCm39) R152W probably damaging Het
Aldh1a2 A G 9: 71,188,964 (GRCm39) N293D possibly damaging Het
Ash2l T C 8: 26,312,913 (GRCm39) N441S probably damaging Het
Asrgl1 A T 19: 9,093,864 (GRCm39) probably null Het
Capn3 C A 2: 120,316,902 (GRCm39) S277* probably null Het
Ccdc168 A T 1: 44,096,339 (GRCm39) S1586R possibly damaging Het
Ccp110 T C 7: 118,329,167 (GRCm39) probably benign Het
Cdh17 T C 4: 11,799,676 (GRCm39) V491A probably benign Het
Cep170b T C 12: 112,707,339 (GRCm39) S362P probably damaging Het
Cfap57 A G 4: 118,463,849 (GRCm39) S335P possibly damaging Het
Cmklr1 A T 5: 113,752,107 (GRCm39) L298Q probably damaging Het
Col4a4 A T 1: 82,466,730 (GRCm39) probably null Het
Cul9 C G 17: 46,833,101 (GRCm39) A1326P probably damaging Het
Cyp2d26 A G 15: 82,677,068 (GRCm39) probably benign Het
Cyth3 T C 5: 143,688,575 (GRCm39) Y240H probably damaging Het
Dhx9 G A 1: 153,334,109 (GRCm39) T1017I probably damaging Het
Edar T C 10: 58,464,453 (GRCm39) Y62C probably damaging Het
Esyt3 C T 9: 99,200,097 (GRCm39) G699D possibly damaging Het
Fgb T C 3: 82,950,564 (GRCm39) T397A probably damaging Het
Foxc1 C A 13: 31,992,668 (GRCm39) A493E unknown Het
Grid1 T C 14: 34,542,186 (GRCm39) M1T probably null Het
Ipo4 T C 14: 55,871,816 (GRCm39) K113R probably damaging Het
Kif21b A G 1: 136,080,114 (GRCm39) E550G probably damaging Het
Krt1 T C 15: 101,757,416 (GRCm39) K265E possibly damaging Het
Mcm5 A G 8: 75,852,919 (GRCm39) K677R probably benign Het
Metap1 A T 3: 138,180,791 (GRCm39) L130* probably null Het
Mrgpra4 A G 7: 47,631,085 (GRCm39) L172P probably benign Het
Mylip G A 13: 45,560,178 (GRCm39) E205K probably damaging Het
Myo3b A C 2: 70,161,224 (GRCm39) E1128A probably benign Het
Naip2 T C 13: 100,298,362 (GRCm39) E558G probably benign Het
Naip2 C T 13: 100,298,368 (GRCm39) G556D probably benign Het
Nlrp4d T C 7: 10,098,194 (GRCm39) I823V probably benign Het
Odad1 C T 7: 45,592,182 (GRCm39) probably benign Het
Rec114 A T 9: 58,573,103 (GRCm39) probably benign Het
Rimbp2 C T 5: 128,865,351 (GRCm39) A666T probably benign Het
Siva1 C T 12: 112,613,355 (GRCm39) Q68* probably null Het
Slc22a27 T A 19: 7,904,033 (GRCm39) I35F probably benign Het
Slco1a5 T A 6: 142,200,100 (GRCm39) N228I probably damaging Het
St8sia4 G A 1: 95,581,464 (GRCm39) R93C probably damaging Het
Tprg1 T C 16: 25,231,593 (GRCm39) S190P probably damaging Het
Trpc6 A G 9: 8,658,287 (GRCm39) probably null Het
Vmn2r70 C T 7: 85,208,269 (GRCm39) C736Y probably damaging Het
Zfp629 C T 7: 127,211,916 (GRCm39) probably benign Het
Zswim4 A G 8: 84,946,601 (GRCm39) V685A possibly 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
R2897:Lmx1a UTSW 1 167,658,109 (GRCm39) splice site probably benign
R4211:Lmx1a UTSW 1 167,660,428 (GRCm39) missense probably damaging 0.96
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'- TGCACCAGTACAAACATTCCTGTCC -3'
(R):5'- GCAGAGAATTGCCTTGCCATAGACC -3'

Sequencing Primer
(F):5'- CATTCCTGTCCCAGGGTTGAAG -3'
(R):5'- AAGGCACTCACCTGAGTCTG -3'
Posted On 2014-01-15