Incidental Mutation 'R6262:Lhx3'
ID 506736
Institutional Source Beutler Lab
Gene Symbol Lhx3
Ensembl Gene ENSMUSG00000026934
Gene Name LIM homeobox protein 3
Synonyms Lim3, mLim-3, P-LIM
MMRRC Submission 045016-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6262 (G1)
Quality Score 217.468
Status Validated
Chromosome 2
Chromosomal Location 26090224-26098261 bp(-) (GRCm39)
Type of Mutation small deletion (1 aa in frame mutation)
DNA Base Change (assembly) GTGTTGT to GTGT at 26092435 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000056822 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028302] [ENSMUST00000054099]
AlphaFold P50481
PDB Structure NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000028302
SMART Domains Protein: ENSMUSP00000028302
Gene: ENSMUSG00000026934

DomainStartEndE-ValueType
low complexity region 14 31 N/A INTRINSIC
LIM 35 86 4.18e-17 SMART
LIM 94 149 7.8e-17 SMART
HOX 162 224 7.13e-23 SMART
low complexity region 237 249 N/A INTRINSIC
low complexity region 323 342 N/A INTRINSIC
low complexity region 353 362 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000054099
SMART Domains Protein: ENSMUSP00000056822
Gene: ENSMUSG00000026934

DomainStartEndE-ValueType
LIM 33 84 4.18e-17 SMART
LIM 92 147 7.8e-17 SMART
HOX 160 222 7.13e-23 SMART
low complexity region 235 247 N/A INTRINSIC
low complexity region 321 340 N/A INTRINSIC
low complexity region 351 360 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127035
SMART Domains Protein: ENSMUSP00000134884
Gene: ENSMUSG00000026934

DomainStartEndE-ValueType
Pfam:Homeobox 1 17 6.2e-5 PFAM
low complexity region 35 47 N/A INTRINSIC
low complexity region 121 140 N/A INTRINSIC
low complexity region 151 160 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149637
SMART Domains Protein: ENSMUSP00000135765
Gene: ENSMUSG00000026934

DomainStartEndE-ValueType
low complexity region 2 16 N/A INTRINSIC
low complexity region 22 38 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184787
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.6%
  • 20x: 96.2%
Validation Efficiency 97% (58/60)
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 family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failure of growth and differentiation of Rathke's pouch, lack both anterior and intermediate lobes of the pituitary gland, and die perinatally, within 24 hours of birth. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca1 G A 4: 53,092,917 (GRCm39) T289I probably benign Het
Abca2 T C 2: 25,334,922 (GRCm39) Y1965H possibly damaging Het
Adam26a T C 8: 44,022,125 (GRCm39) N455S possibly damaging Het
Art5 C T 7: 101,747,338 (GRCm39) G147D probably benign Het
Atp5f1a G A 18: 77,868,912 (GRCm39) V429M probably damaging Het
Calr4 A T 4: 109,108,564 (GRCm39) N213I probably damaging Het
Cchcr1 T C 17: 35,841,413 (GRCm39) S810P probably benign Het
Cdh4 A T 2: 179,439,419 (GRCm39) R189W probably damaging Het
Cdk5rap1 T C 2: 154,212,606 (GRCm39) D84G probably benign Het
Clasp2 T A 9: 113,705,420 (GRCm39) probably null Het
Cntnap2 T A 6: 45,037,046 (GRCm39) probably null Het
Cntnap4 T C 8: 113,529,843 (GRCm39) Y684H probably damaging Het
Cyp2a4 T A 7: 26,011,655 (GRCm39) V292E probably damaging Het
Dap A G 15: 31,235,960 (GRCm39) T10A probably benign Het
Dnah11 G A 12: 117,894,913 (GRCm39) R3645C probably damaging Het
Dnah9 A T 11: 65,772,631 (GRCm39) probably null Het
Efcab3 T A 11: 104,784,579 (GRCm39) M2787K probably benign Het
Efr3a T C 15: 65,729,323 (GRCm39) S675P possibly damaging Het
Gria1 A G 11: 57,133,680 (GRCm39) K451E probably damaging Het
Grin3b A T 10: 79,810,203 (GRCm39) M570L probably benign Het
Hs2st1 A G 3: 144,140,374 (GRCm39) F316L probably damaging Het
Hs6st3 A G 14: 119,376,403 (GRCm39) T193A possibly damaging Het
Hspg2 A T 4: 137,246,997 (GRCm39) D1108V probably damaging Het
Igf1r T A 7: 67,653,720 (GRCm39) L86Q probably damaging Het
Inpp5j A G 11: 3,452,615 (GRCm39) S212P probably benign Het
Junb A G 8: 85,704,359 (GRCm39) S234P possibly damaging Het
Macf1 A G 4: 123,366,983 (GRCm39) S1028P possibly damaging Het
Met C A 6: 17,553,403 (GRCm39) A1063E probably benign Het
Mink1 T C 11: 70,494,151 (GRCm39) probably null Het
Mtor A G 4: 148,610,552 (GRCm39) E1621G possibly damaging Het
Mug2 T C 6: 122,052,214 (GRCm39) Y991H probably damaging Het
Neb T C 2: 52,198,699 (GRCm39) D414G probably damaging Het
Nkx6-3 T C 8: 23,643,863 (GRCm39) V88A probably benign Het
Nr3c2 A G 8: 77,635,262 (GRCm39) Q121R possibly damaging Het
Nup155 T C 15: 8,186,225 (GRCm39) V1329A probably benign Het
Or2d36 T C 7: 106,746,918 (GRCm39) Y132H probably damaging Het
Or5d35 T C 2: 87,855,738 (GRCm39) V224A probably benign Het
Pcdhb17 T A 18: 37,619,751 (GRCm39) F514I probably damaging Het
Pfkl A G 10: 77,824,507 (GRCm39) probably null Het
Prl8a1 A T 13: 27,758,126 (GRCm39) H194Q possibly damaging Het
Sh3tc1 C G 5: 35,857,117 (GRCm39) E1241Q probably damaging Het
Slc6a6 A T 6: 91,732,013 (GRCm39) H614L possibly damaging Het
Sort1 A G 3: 108,217,527 (GRCm39) Y143C probably damaging Het
Stat4 T A 1: 52,141,360 (GRCm39) W569R probably null Het
Taco1 A T 11: 105,962,693 (GRCm39) K127* probably null Het
Tas2r110 T C 6: 132,845,638 (GRCm39) I223T probably damaging Het
Tex21 A G 12: 76,259,306 (GRCm39) I329T probably damaging Het
Tmprss11b T C 5: 86,810,119 (GRCm39) H287R probably benign Het
Trim30a A G 7: 104,060,741 (GRCm39) L345P probably benign Het
Vmn1r62 G A 7: 5,678,556 (GRCm39) C79Y probably damaging Het
Vmn2r116 A G 17: 23,606,351 (GRCm39) K421R probably benign Het
Vwde C T 6: 13,205,020 (GRCm39) S287N probably damaging Het
Xrcc4 A T 13: 89,926,906 (GRCm39) M300K probably benign Het
Zan A T 5: 137,427,747 (GRCm39) probably null Het
Zbtb7c A G 18: 76,270,413 (GRCm39) D167G probably benign Het
Zfc3h1 A G 10: 115,249,881 (GRCm39) Y1165C probably damaging Het
Zfp326 T A 5: 106,036,353 (GRCm39) L88Q probably damaging Het
Zfp667 A G 7: 6,307,973 (GRCm39) T214A probably benign Het
Other mutations in Lhx3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02309:Lhx3 APN 2 26,091,385 (GRCm39) missense probably benign
IGL02691:Lhx3 APN 2 26,093,097 (GRCm39) missense probably damaging 1.00
R0267:Lhx3 UTSW 2 26,093,040 (GRCm39) missense probably benign 0.02
R0571:Lhx3 UTSW 2 26,091,136 (GRCm39) missense probably damaging 1.00
R0574:Lhx3 UTSW 2 26,091,323 (GRCm39) missense probably benign 0.00
R1866:Lhx3 UTSW 2 26,093,986 (GRCm39) missense probably damaging 0.99
R1926:Lhx3 UTSW 2 26,092,200 (GRCm39) nonsense probably null
R1940:Lhx3 UTSW 2 26,093,974 (GRCm39) missense probably benign 0.05
R3147:Lhx3 UTSW 2 26,091,277 (GRCm39) missense probably benign 0.01
R4389:Lhx3 UTSW 2 26,091,102 (GRCm39) utr 3 prime probably benign
R4534:Lhx3 UTSW 2 26,094,026 (GRCm39) missense probably benign
R4551:Lhx3 UTSW 2 26,091,202 (GRCm39) missense probably damaging 1.00
R4761:Lhx3 UTSW 2 26,091,435 (GRCm39) frame shift probably null
R5102:Lhx3 UTSW 2 26,091,435 (GRCm39) frame shift probably null
R5105:Lhx3 UTSW 2 26,091,435 (GRCm39) frame shift probably null
R5431:Lhx3 UTSW 2 26,091,130 (GRCm39) missense probably damaging 1.00
R5673:Lhx3 UTSW 2 26,093,006 (GRCm39) missense probably damaging 1.00
R5751:Lhx3 UTSW 2 26,091,173 (GRCm39) missense probably benign
R6180:Lhx3 UTSW 2 26,091,503 (GRCm39) missense probably benign
R7238:Lhx3 UTSW 2 26,093,009 (GRCm39) missense probably damaging 1.00
R8934:Lhx3 UTSW 2 26,092,258 (GRCm39) missense probably damaging 0.98
Z1176:Lhx3 UTSW 2 26,093,999 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATTCTGGAACCACACCTGGG -3'
(R):5'- GGTTCCTAATACAGAGCCCG -3'

Sequencing Primer
(F):5'- GGGGTAGGGATGGTGAGTGAC -3'
(R):5'- CATGGGCATCCGGAGATC -3'
Posted On 2018-03-15