Incidental Mutation 'R5125:Lmx1a'
ID 393480
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 042713-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.883) question?
Stock # R5125 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 167516806-167676310 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 167658256 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 213 (S213L)
Ref Sequence ENSEMBL: ENSMUSP00000107008 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028003] [ENSMUST00000111377]
AlphaFold Q9JKU8
Predicted Effect possibly damaging
Transcript: ENSMUST00000028003
AA Change: S213L

PolyPhen 2 Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: S213L

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 possibly damaging
Transcript: ENSMUST00000111377
AA Change: S213L

PolyPhen 2 Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: S213L

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 0.2795 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.9%
Validation Efficiency 96% (49/51)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abt1 G T 13: 23,606,819 (GRCm39) A94E possibly damaging Het
Carmil2 G T 8: 106,423,521 (GRCm39) G1207V probably damaging Het
Cyp2c66 A G 19: 39,159,473 (GRCm39) Y308C probably damaging Het
Dcc A G 18: 71,589,948 (GRCm39) F683L probably benign Het
Denr A T 5: 124,065,144 (GRCm39) I166F probably damaging Het
Dhx29 T G 13: 113,069,134 (GRCm39) S155A possibly damaging Het
Dsg1b G A 18: 20,530,560 (GRCm39) G405E probably damaging Het
Ei24 T A 9: 36,693,742 (GRCm39) probably benign Het
Exo5 A T 4: 120,778,734 (GRCm39) probably null Het
Gm7356 T C 17: 14,221,576 (GRCm39) D151G probably damaging Het
Grin1 T C 2: 25,186,839 (GRCm39) probably benign Het
Grin2b C T 6: 135,900,297 (GRCm39) V195M possibly damaging Het
Hephl1 T A 9: 14,997,468 (GRCm39) K399N probably damaging Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Kmt2c A G 5: 25,489,379 (GRCm39) V4520A probably damaging Het
Lair1 G A 7: 4,013,488 (GRCm39) T82I possibly damaging Het
Ly6g6d A G 17: 35,293,418 (GRCm39) I8T possibly damaging Het
Mcm4 T A 16: 15,453,167 (GRCm39) D174V probably benign Het
Mcph1 T A 8: 18,657,342 (GRCm39) D60E probably damaging Het
Med12l G A 3: 59,174,635 (GRCm39) G1851D possibly damaging Het
Or13c7b T A 4: 43,820,480 (GRCm39) I294F probably benign Het
Or7e174 T A 9: 20,012,488 (GRCm39) C144* probably null Het
P2rx2 G A 5: 110,490,517 (GRCm39) T66I possibly damaging Het
Pcdh15 A G 10: 74,419,912 (GRCm39) E1197G probably damaging Het
Pira1 T A 7: 3,742,396 (GRCm39) K44* probably null Het
Ppwd1 A T 13: 104,356,943 (GRCm39) S191T probably benign Het
Rbm39 A T 2: 156,004,785 (GRCm39) M184K probably damaging Het
Reln A G 5: 22,118,239 (GRCm39) V2935A possibly damaging Het
Robo4 T C 9: 37,319,256 (GRCm39) W535R probably damaging Het
Rsf1 A G 7: 97,311,079 (GRCm39) D603G possibly damaging Het
Sh3rf3 C G 10: 58,967,012 (GRCm39) P785A probably benign Het
Slc22a26 T C 19: 7,767,540 (GRCm39) T289A possibly damaging Het
Slc24a3 T C 2: 145,360,767 (GRCm39) V120A possibly damaging Het
Sost C T 11: 101,854,767 (GRCm39) G181R probably damaging Het
Sp2 A G 11: 96,846,664 (GRCm39) F554L probably benign Het
Stim2 T C 5: 54,267,939 (GRCm39) S87P probably damaging Het
Tecta T C 9: 42,286,481 (GRCm39) D725G probably damaging Het
Trgc4 A G 13: 19,528,932 (GRCm39) probably benign Het
Ube4b T C 4: 149,427,449 (GRCm39) M900V probably damaging Het
Ugt2b38 A G 5: 87,559,671 (GRCm39) M407T probably damaging Het
Vmn1r87 G T 7: 12,865,792 (GRCm39) A165E possibly damaging Het
Zc3h6 A G 2: 128,856,399 (GRCm39) H493R possibly damaging Het
Zfhx2 A T 14: 55,312,232 (GRCm39) F154Y probably benign Het
Zfp729a A G 13: 67,785,764 (GRCm39) probably null Het
Zfp976 A G 7: 42,261,925 (GRCm39) probably null Het
Zhx1 C G 15: 57,917,470 (GRCm39) G259R probably damaging Het
Znfx1 A T 2: 166,888,859 (GRCm39) V783E 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
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
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
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'- CCAGAGCTTATCTTGGAGCAAC -3'
(R):5'- GGGCTCATAACTGTCACAGAC -3'

Sequencing Primer
(F):5'- CTTATCTTGGAGCAACAAAAGGC -3'
(R):5'- GGCTCATAACTGTCACAGACTCTGAG -3'
Posted On 2016-06-15