Incidental Mutation 'R3721:Lhx1'
ID 258924
Institutional Source Beutler Lab
Gene Symbol Lhx1
Ensembl Gene ENSMUSG00000018698
Gene Name LIM homeobox protein 1
Synonyms Lim1
MMRRC Submission 040712-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3721 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 84409110-84416361 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 84412654 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 89 (R89C)
Ref Sequence ENSEMBL: ENSMUSP00000138899 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018842] [ENSMUST00000092827] [ENSMUST00000184646]
AlphaFold P63006
Predicted Effect probably damaging
Transcript: ENSMUST00000018842
AA Change: R180C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000018842
Gene: ENSMUSG00000018698
AA Change: R180C

DomainStartEndE-ValueType
LIM 3 54 5.51e-17 SMART
LIM 62 117 4.24e-18 SMART
low complexity region 137 156 N/A INTRINSIC
HOX 180 242 1.33e-22 SMART
low complexity region 315 327 N/A INTRINSIC
low complexity region 349 367 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000092827
SMART Domains Protein: ENSMUSP00000090503
Gene: ENSMUSG00000018698

DomainStartEndE-ValueType
LIM 18 73 4.24e-18 SMART
low complexity region 93 112 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126072
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128121
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134800
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176503
SMART Domains Protein: ENSMUSP00000135334
Gene: ENSMUSG00000018698

DomainStartEndE-ValueType
Pfam:Homeobox 1 17 5.3e-6 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000184646
AA Change: R89C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000138899
Gene: ENSMUSG00000018698
AA Change: R89C

DomainStartEndE-ValueType
low complexity region 46 65 N/A INTRINSIC
HOX 89 151 6.8e-25 SMART
low complexity region 224 236 N/A INTRINSIC
low complexity region 258 276 N/A INTRINSIC
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.2%
Validation Efficiency 100% (59/59)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]
PHENOTYPE: Homozygotes for targeted null mutations are small, fail to develop head structures anterior to rhombomere 3 in the hindbrain, lack kidneys and gonads, and show aberrant trajectories of limb motor axons. Most mutants die around embryonic day 10. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acvr2a T C 2: 48,782,150 (GRCm39) S228P probably damaging Het
Adamts2 C T 11: 50,664,038 (GRCm39) probably benign Het
Arhgap9 A G 10: 127,164,840 (GRCm39) E588G possibly damaging Het
Ash2l C G 8: 26,308,653 (GRCm39) G453A probably damaging Het
Catsperg2 A G 7: 29,404,527 (GRCm39) V638A probably benign Het
Ccrl2 T C 9: 110,885,432 (GRCm39) D22G probably benign Het
Cdc73 T C 1: 143,571,191 (GRCm39) I83V possibly damaging Het
Ceacam23 A G 7: 17,636,663 (GRCm39) T247A probably benign Het
Clec2e C A 6: 129,071,373 (GRCm39) E155* probably null Het
Cyp3a59 T A 5: 146,033,407 (GRCm39) M181K probably damaging Het
Dars2 A T 1: 160,890,878 (GRCm39) V111E probably benign Het
Diras2 T A 13: 52,662,059 (GRCm39) I83F probably damaging Het
Dlg2 T A 7: 91,361,008 (GRCm39) probably null Het
Dnai1 G A 4: 41,602,615 (GRCm39) R113H probably damaging Het
Eeig2 C T 3: 108,887,083 (GRCm39) R305Q probably damaging Het
Emilin2 T C 17: 71,580,449 (GRCm39) N759S probably benign Het
F11 A G 8: 45,701,675 (GRCm39) S353P probably damaging Het
Ggnbp1 T C 17: 27,248,587 (GRCm39) V52A probably benign Het
Gpr171 A G 3: 59,005,091 (GRCm39) V228A possibly damaging Het
Gsta3 T C 1: 21,330,313 (GRCm39) M55T probably benign Het
Hectd3 T A 4: 116,856,942 (GRCm39) N496K probably benign Het
Hp1bp3 T G 4: 137,966,919 (GRCm39) F367V probably damaging Het
Il18rap T A 1: 40,576,248 (GRCm39) L253Q probably damaging Het
Irs1 C T 1: 82,267,806 (GRCm39) G137S probably benign Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lair1 A C 7: 4,013,782 (GRCm39) L155R probably damaging Het
Larp7 A G 3: 127,340,460 (GRCm39) L126P probably damaging Het
Lypd4 C A 7: 24,564,884 (GRCm39) A85S probably benign Het
Mei1 A G 15: 81,987,405 (GRCm39) H399R possibly damaging Het
Myh10 G T 11: 68,703,878 (GRCm39) R1863L probably damaging Het
Myo9a G A 9: 59,775,463 (GRCm39) V1025I probably benign Het
Naa25 T A 5: 121,569,619 (GRCm39) D659E probably benign Het
Nol9 A G 4: 152,124,163 (GRCm39) S118G probably benign Het
Or4k2 C T 14: 50,424,137 (GRCm39) C179Y probably damaging Het
Or5p72 G T 7: 108,022,326 (GRCm39) D183Y probably damaging Het
Pde10a T A 17: 9,188,421 (GRCm39) I907N probably damaging Het
Pkhd1 T C 1: 20,655,879 (GRCm39) D218G probably benign Het
Poll A G 19: 45,542,016 (GRCm39) I430T probably damaging Het
Pomgnt1 T G 4: 116,010,740 (GRCm39) probably benign Het
Rab6b T C 9: 103,044,373 (GRCm39) probably null Het
Rad1 T C 15: 10,488,112 (GRCm39) S79P probably benign Het
Ranbp17 GCCTGGATACTGACC GCC 11: 33,169,203 (GRCm39) probably benign Het
Rcc1 T C 4: 132,065,125 (GRCm39) K133E possibly damaging Het
Ric8a T C 7: 140,441,874 (GRCm39) probably null Het
Rnf135 G T 11: 80,087,743 (GRCm39) A231S probably benign Het
Rps6ka4 A G 19: 6,816,645 (GRCm39) V146A possibly damaging Het
Sh3bp4 A G 1: 89,073,050 (GRCm39) I633V possibly damaging Het
Slc2a2 T A 3: 28,781,301 (GRCm39) N446K probably damaging Het
Slc44a1 T C 4: 53,491,445 (GRCm39) Y61H probably damaging Het
Slc7a1 G A 5: 148,272,343 (GRCm39) R445* probably null Het
Smc5 T C 19: 23,187,856 (GRCm39) M911V probably benign Het
Sntb1 C A 15: 55,506,214 (GRCm39) R453L probably benign Het
Spink4 T A 4: 40,929,136 (GRCm39) C54S probably damaging Het
Srrm2 CTCCTCTTCTTCCTCTTCTTCCTC CTCCTCTTCTTCCTC 17: 24,041,549 (GRCm39) probably benign Het
Trpm1 T G 7: 63,867,475 (GRCm39) probably benign Het
Tufm T C 7: 126,089,632 (GRCm39) M442T probably benign Het
Ubn1 A G 16: 4,891,242 (GRCm39) N539S possibly damaging Het
Other mutations in Lhx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00757:Lhx1 APN 11 84,410,478 (GRCm39) missense probably damaging 0.97
R1346:Lhx1 UTSW 11 84,412,905 (GRCm39) missense possibly damaging 0.55
R1565:Lhx1 UTSW 11 84,410,647 (GRCm39) missense probably benign 0.00
R1806:Lhx1 UTSW 11 84,414,967 (GRCm39) missense probably damaging 1.00
R2148:Lhx1 UTSW 11 84,410,647 (GRCm39) missense probably benign 0.00
R2449:Lhx1 UTSW 11 84,412,564 (GRCm39) missense probably damaging 1.00
R3793:Lhx1 UTSW 11 84,412,726 (GRCm39) missense probably benign 0.01
R4940:Lhx1 UTSW 11 84,410,735 (GRCm39) nonsense probably null
R5178:Lhx1 UTSW 11 84,411,214 (GRCm39) missense possibly damaging 0.69
R5877:Lhx1 UTSW 11 84,413,065 (GRCm39) missense probably damaging 1.00
R6366:Lhx1 UTSW 11 84,413,034 (GRCm39) missense probably damaging 1.00
R6551:Lhx1 UTSW 11 84,412,739 (GRCm39) missense probably benign 0.23
R7060:Lhx1 UTSW 11 84,411,108 (GRCm39) critical splice donor site probably null
R7106:Lhx1 UTSW 11 84,412,903 (GRCm39) missense probably benign 0.00
R7133:Lhx1 UTSW 11 84,410,746 (GRCm39) missense probably benign 0.00
R7161:Lhx1 UTSW 11 84,410,698 (GRCm39) missense probably damaging 1.00
R7290:Lhx1 UTSW 11 84,412,703 (GRCm39) missense probably damaging 0.96
R8843:Lhx1 UTSW 11 84,410,455 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- TGGCCATTCGAGTCTTTGAG -3'
(R):5'- GGATTCCCAACTGGCTAGAG -3'

Sequencing Primer
(F):5'- TCTTTGAGAGACAGAGTGACAAACC -3'
(R):5'- CCAACTGGCTAGAGGGTGG -3'
Posted On 2015-01-23