Incidental Mutation 'R6858:Lmx1a'
ID 535348
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 044960-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.883) question?
Stock # R6858 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 167516806-167676310 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 167660450 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 245 (N245I)
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: N245I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: N245I

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: N245I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: N245I

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: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.4%
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aldob T C 4: 49,538,796 (GRCm39) T241A probably benign Het
Arid4a A G 12: 71,070,283 (GRCm39) I65V probably benign Het
Bhmt2 C T 13: 93,807,948 (GRCm39) E47K probably damaging Het
Bpifa3 G A 2: 153,979,514 (GRCm39) G213D probably benign Het
C4b C G 17: 34,948,805 (GRCm39) A1548P probably damaging Het
Ccdc39 A G 3: 33,874,017 (GRCm39) V605A probably damaging Het
Cept1 A T 3: 106,420,195 (GRCm39) probably null Het
Cntrl T C 2: 35,052,107 (GRCm39) probably null Het
Col3a1 A G 1: 45,385,144 (GRCm39) D87G probably damaging Het
Crim1 A T 17: 78,623,056 (GRCm39) E418V probably damaging Het
Crtac1 T C 19: 42,307,174 (GRCm39) I196M possibly damaging Het
Crtap T C 9: 114,209,084 (GRCm39) Y320C probably damaging Het
Cttnbp2 A G 6: 18,448,452 (GRCm39) V27A probably damaging Het
Cyp2c69 G A 19: 39,866,009 (GRCm39) L195F probably benign Het
Cyp2d26 G A 15: 82,678,284 (GRCm39) R31C probably damaging Het
Fan1 T A 7: 64,022,234 (GRCm39) N340Y probably damaging Het
Fign G T 2: 63,810,157 (GRCm39) T371K probably benign Het
Fryl T C 5: 73,222,375 (GRCm39) T2069A probably damaging Het
Gm3486 A G 14: 41,210,322 (GRCm39) I53T probably damaging Het
Gprc5d T C 6: 135,093,313 (GRCm39) N198S possibly damaging Het
Ighv1-42 A G 12: 114,900,966 (GRCm39) S40P probably damaging Het
Itga8 A G 2: 12,204,892 (GRCm39) V515A probably benign Het
Kidins220 A T 12: 25,058,542 (GRCm39) I523L possibly damaging Het
Med22 T C 2: 26,795,949 (GRCm39) D157G possibly damaging Het
Ola1 T C 2: 72,927,574 (GRCm39) H335R probably damaging Het
Or1a1 A T 11: 74,086,925 (GRCm39) M199L probably benign Het
Or4c12 A G 2: 89,774,087 (GRCm39) I124T probably damaging Het
Or6c213 A G 10: 129,574,333 (GRCm39) F151S probably damaging Het
Or7e166 T C 9: 19,624,765 (GRCm39) I214T probably damaging Het
Or8h9 A G 2: 86,789,034 (GRCm39) I256T probably benign Het
Pde1a T A 2: 79,959,502 (GRCm39) probably benign Het
Pdgfrb G A 18: 61,198,219 (GRCm39) G304D probably benign Het
Potegl T C 2: 23,102,676 (GRCm39) V138A possibly damaging Het
Prune2 T A 19: 17,095,470 (GRCm39) C325S possibly damaging Het
Ptk2b T C 14: 66,450,847 (GRCm39) I40V probably damaging Het
Qrich1 A G 9: 108,411,333 (GRCm39) D286G probably damaging Het
Scn5a T C 9: 119,321,156 (GRCm39) I1469V probably benign Het
Serpina3k G A 12: 104,311,504 (GRCm39) A361T possibly damaging Het
Slc25a23 A G 17: 57,365,171 (GRCm39) Y73H probably damaging Het
Tmco3 A G 8: 13,363,924 (GRCm39) D82G probably damaging Het
Trbv28 G T 6: 41,248,624 (GRCm39) M51I probably damaging Het
Unc13b A T 4: 43,165,828 (GRCm39) H204L possibly damaging Het
Vamp5 G A 6: 72,357,424 (GRCm39) probably benign Het
Vmn1r25 T C 6: 57,955,996 (GRCm39) S98G probably benign Het
Vmn2r2 A G 3: 64,044,915 (GRCm39) F77S probably damaging Het
Vmn2r79 A T 7: 86,686,580 (GRCm39) M654L probably benign Het
Zfp985 A T 4: 147,667,764 (GRCm39) K211* probably null Het
Zwilch C T 9: 64,060,869 (GRCm39) D328N 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
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
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'- TAACACAGACACTTCGCTTCTC -3'

Sequencing Primer
(F):5'- GGCACCACCCAGGAAATG -3'
(R):5'- TTCCTCCAGGCGCTGTG -3'
Posted On 2018-09-12