Incidental Mutation 'R0320:Lmx1a'
ID 38262
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 038530-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.882) question?
Stock # R0320 (G1)
Quality Score 195
Status Validated
Chromosome 1
Chromosomal Location 167516806-167676310 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 167618973 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Stop codon at position 111 (Q111*)
Ref Sequence ENSEMBL: ENSMUSP00000107008 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028003] [ENSMUST00000111377]
AlphaFold Q9JKU8
Predicted Effect probably null
Transcript: ENSMUST00000028003
AA Change: Q111*
SMART Domains Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: Q111*

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 null
Transcript: ENSMUST00000111377
AA Change: Q111*
SMART Domains Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: Q111*

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 0.9715 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.0%
Validation Efficiency 100% (71/71)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik T C 14: 32,384,571 (GRCm39) T465A probably benign Het
A430110L20Rik T G 1: 181,054,987 (GRCm39) noncoding transcript Het
Aadacl4fm1 A T 4: 144,248,990 (GRCm39) H119L probably damaging Het
Abcb10 C T 8: 124,689,746 (GRCm39) R439Q probably benign Het
Abcb8 T C 5: 24,605,788 (GRCm39) S199P probably damaging Het
Adam8 C A 7: 139,566,355 (GRCm39) C556F probably damaging Het
Akap11 T C 14: 78,750,819 (GRCm39) T523A probably benign Het
Aldh3b1 T C 19: 3,968,999 (GRCm39) probably benign Het
Arhgap30 T A 1: 171,231,372 (GRCm39) W230R possibly damaging Het
Atp8b4 A G 2: 126,301,614 (GRCm39) I82T possibly damaging Het
Bptf A T 11: 106,963,645 (GRCm39) L1850I probably damaging Het
C4b C A 17: 34,952,135 (GRCm39) V1237L probably benign Het
Calu C A 6: 29,374,550 (GRCm39) probably benign Het
Cit C A 5: 116,117,504 (GRCm39) L1227M possibly damaging Het
Col4a1 C T 8: 11,292,782 (GRCm39) probably null Het
Cp T C 3: 20,029,012 (GRCm39) probably benign Het
Cpd T C 11: 76,731,273 (GRCm39) D311G possibly damaging Het
Ctc1 T A 11: 68,924,363 (GRCm39) S972T probably damaging Het
Dnah17 A G 11: 117,943,500 (GRCm39) F3201L possibly damaging Het
Dop1b C A 16: 93,607,035 (GRCm39) R2113S probably benign Het
Dym T A 18: 75,332,333 (GRCm39) D520E probably damaging Het
Eif5a G T 11: 69,808,305 (GRCm39) T64K probably benign Het
Flt3 A T 5: 147,306,389 (GRCm39) probably benign Het
Ints6 A T 14: 62,945,084 (GRCm39) Y415* probably null Het
Itga1 A G 13: 115,114,130 (GRCm39) probably benign Het
Itgae A G 11: 73,021,825 (GRCm39) H902R possibly damaging Het
Itprid1 T C 6: 55,953,432 (GRCm39) I916T probably damaging Het
Kdm5a T C 6: 120,366,581 (GRCm39) I406T probably benign Het
Lrrc25 T C 8: 71,070,896 (GRCm39) Y226H probably benign Het
Mcam T A 9: 44,051,483 (GRCm39) N447K possibly damaging Het
Mcm10 A T 2: 5,008,897 (GRCm39) D357E probably benign Het
Nrip1 T C 16: 76,089,251 (GRCm39) T769A probably benign Het
Ofcc1 G C 13: 40,360,172 (GRCm39) Q286E probably benign Het
Or1e23 T G 11: 73,407,750 (GRCm39) I92L probably damaging Het
Or56b35 A T 7: 104,963,861 (GRCm39) I217F probably benign Het
Parp3 T A 9: 106,353,011 (GRCm39) N55I possibly damaging Het
Parp4 T C 14: 56,825,953 (GRCm39) probably null Het
Pilrb1 G A 5: 137,853,260 (GRCm39) T181I probably benign Het
Ppm1n A G 7: 19,012,281 (GRCm39) V317A probably damaging Het
Prdm2 A T 4: 142,905,921 (GRCm39) F55L probably damaging Het
Psd2 C T 18: 36,112,697 (GRCm39) R131C probably damaging Het
Ralgps1 A T 2: 33,031,027 (GRCm39) C570S possibly damaging Het
Scaf8 T C 17: 3,228,530 (GRCm39) S443P unknown Het
Setd5 A G 6: 113,088,442 (GRCm39) K190R probably damaging Het
Spsb4 T A 9: 96,878,161 (GRCm39) H54L probably damaging Het
St7l T A 3: 104,778,229 (GRCm39) L122* probably null Het
Stom C T 2: 35,211,646 (GRCm39) R125H probably damaging Het
Tigd4 T A 3: 84,502,481 (GRCm39) V466E probably benign Het
Tmc3 A C 7: 83,257,027 (GRCm39) probably benign Het
Vcl C T 14: 21,035,692 (GRCm39) probably benign Het
Vmn1r168 G A 7: 23,240,767 (GRCm39) R208H probably benign Het
Vmn2r75 C A 7: 85,814,288 (GRCm39) V402L probably benign Het
Vps13b A T 15: 35,674,974 (GRCm39) H1698L probably damaging Het
Wnt16 T G 6: 22,297,992 (GRCm39) V286G possibly damaging Het
Xirp1 C A 9: 119,845,533 (GRCm39) V1117L probably benign Het
Zfp788 C T 7: 41,298,971 (GRCm39) H536Y 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
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
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'- ATGGACCACCTTCCCCG -3'
Posted On 2013-05-23