Incidental Mutation 'IGL02309:Lhx3'
ID 287743
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lhx3
Ensembl Gene ENSMUSG00000026934
Gene Name LIM homeobox protein 3
Synonyms Lim3, mLim-3, P-LIM
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02309
Quality Score
Status
Chromosome 2
Chromosomal Location 26090224-26098261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 26091385 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 308 (Q308R)
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
AA Change: Q310R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000028302
Gene: ENSMUSG00000026934
AA Change: Q310R

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
AA Change: Q308R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000056822
Gene: ENSMUSG00000026934
AA Change: Q308R

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
Coding Region Coverage
Validation Efficiency
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg4 A G 9: 44,193,125 (GRCm39) F111S probably benign Het
Afg1l C A 10: 42,330,374 (GRCm39) V98F possibly damaging Het
Agk T A 6: 40,353,210 (GRCm39) D191E possibly damaging Het
Akap5 A G 12: 76,375,629 (GRCm39) K354E possibly damaging Het
Aplp2 A T 9: 31,078,979 (GRCm39) M323K possibly damaging Het
Arhgap23 T C 11: 97,356,827 (GRCm39) probably benign Het
Asl A G 5: 130,048,622 (GRCm39) Y30H probably damaging Het
Asxl3 T A 18: 22,655,510 (GRCm39) H1173Q probably benign Het
Celsr2 C T 3: 108,303,327 (GRCm39) R2472H probably damaging Het
Clip1 T A 5: 123,755,763 (GRCm39) H950L probably damaging Het
Cx3cl1 A T 8: 95,506,660 (GRCm39) T222S probably benign Het
Cyp4a14 T A 4: 115,348,829 (GRCm39) N273Y probably damaging Het
Ddx52 T A 11: 83,839,304 (GRCm39) S214T probably damaging Het
Dennd2d T A 3: 106,402,284 (GRCm39) M318K probably benign Het
Dock3 A T 9: 106,790,351 (GRCm39) D1E probably damaging Het
Farp1 C T 14: 121,480,928 (GRCm39) T443I probably benign Het
Gm2381 C T 7: 42,472,033 (GRCm39) probably benign Het
Gpr87 T A 3: 59,086,975 (GRCm39) I178F possibly damaging Het
Grin2b C T 6: 135,713,470 (GRCm39) E804K probably damaging Het
Gtf2h1 T C 7: 46,465,812 (GRCm39) L421P probably damaging Het
Haghl T G 17: 26,003,638 (GRCm39) H56P probably damaging Het
Heatr3 T C 8: 88,893,700 (GRCm39) L489P probably damaging Het
Ighv6-6 A T 12: 114,398,534 (GRCm39) H77Q probably benign Het
Kdm2b A G 5: 123,085,883 (GRCm39) S243P probably damaging Het
Lamc3 T C 2: 31,804,616 (GRCm39) probably benign Het
Lgr4 T C 2: 109,842,880 (GRCm39) probably benign Het
Lonp2 G A 8: 87,361,491 (GRCm39) E223K probably damaging Het
Lta4h T C 10: 93,310,352 (GRCm39) F407L probably damaging Het
Mndal C T 1: 173,702,021 (GRCm39) G94R probably damaging Het
Nrxn3 A G 12: 89,943,175 (GRCm39) N101S probably damaging Het
Or14c41 T C 7: 86,234,705 (GRCm39) V74A possibly damaging Het
Or51af1 A T 7: 103,141,206 (GRCm39) I293K probably damaging Het
Or8b48 C T 9: 38,492,809 (GRCm39) P79S probably damaging Het
Or8b48 A G 9: 38,492,729 (GRCm39) N52S probably damaging Het
Or8d23 A G 9: 38,842,348 (GRCm39) N294D probably damaging Het
Pknox1 T G 17: 31,809,683 (GRCm39) F96V probably benign Het
Psg25 T G 7: 18,260,349 (GRCm39) Q183P probably damaging Het
Ptgs2 A G 1: 149,981,307 (GRCm39) Y530C probably damaging Het
Sema3e T A 5: 14,274,404 (GRCm39) D218E probably damaging Het
Shank1 G A 7: 43,962,266 (GRCm39) G46R unknown Het
Sidt1 T C 16: 44,075,343 (GRCm39) I672V probably benign Het
Skic3 A G 13: 76,275,166 (GRCm39) T238A possibly damaging Het
Slco1b2 T A 6: 141,618,007 (GRCm39) S486T probably damaging Het
Smchd1 T C 17: 71,750,898 (GRCm39) H340R probably benign Het
Smoc2 C A 17: 14,595,789 (GRCm39) probably benign Het
Snapc1 A G 12: 74,014,801 (GRCm39) Y102C probably damaging Het
Spo11 A G 2: 172,821,744 (GRCm39) R20G probably damaging Het
Tlr1 A T 5: 65,083,290 (GRCm39) L429* probably null Het
Tmem229b-ps T C 10: 53,351,466 (GRCm39) noncoding transcript Het
Trim12c T A 7: 103,994,163 (GRCm39) E230D possibly damaging Het
Ttc17 G T 2: 94,173,006 (GRCm39) N796K probably benign Het
Ttn A G 2: 76,709,443 (GRCm39) probably benign Het
Ublcp1 A T 11: 44,349,155 (GRCm39) probably benign Het
Usf3 C T 16: 44,021,026 (GRCm39) T11M probably benign Het
Vmn2r115 T A 17: 23,564,113 (GRCm39) M95K probably benign Het
Wapl A G 14: 34,466,820 (GRCm39) T1160A probably damaging Het
Other mutations in Lhx3
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
R6262:Lhx3 UTSW 2 26,092,435 (GRCm39) small deletion 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
Posted On 2015-04-16