Incidental Mutation 'IGL01391:Lhx6'
ID 79215
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lhx6
Ensembl Gene ENSMUSG00000026890
Gene Name LIM homeobox protein 6
Synonyms
Accession Numbers
Essential gene? Probably essential (E-score: 0.926) question?
Stock # IGL01391
Quality Score
Status
Chromosome 2
Chromosomal Location 35971965-35995420 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 35993477 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 74 (C74S)
Ref Sequence ENSEMBL: ENSMUSP00000108591 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000112960] [ENSMUST00000112961] [ENSMUST00000112963] [ENSMUST00000112966] [ENSMUST00000112967] [ENSMUST00000148852]
AlphaFold Q9R1R0
Predicted Effect probably benign
Transcript: ENSMUST00000112960
AA Change: C74S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: C74S

DomainStartEndE-ValueType
low complexity region 71 94 N/A INTRINSIC
LIM 98 151 7.34e-13 SMART
LIM 159 213 3.17e-17 SMART
HOX 248 310 1.1e-23 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112961
AA Change: C45S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: C45S

DomainStartEndE-ValueType
low complexity region 42 65 N/A INTRINSIC
LIM 69 122 7.34e-13 SMART
LIM 130 184 3.17e-17 SMART
HOX 219 281 1.1e-23 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112963
AA Change: C45S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: C45S

DomainStartEndE-ValueType
low complexity region 42 65 N/A INTRINSIC
LIM 69 122 7.34e-13 SMART
LIM 130 184 3.17e-17 SMART
HOX 219 281 1.1e-23 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112966
AA Change: C45S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: C45S

DomainStartEndE-ValueType
low complexity region 42 65 N/A INTRINSIC
LIM 69 122 7.34e-13 SMART
LIM 130 184 3.17e-17 SMART
HOX 219 281 1.1e-23 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112967
AA Change: C74S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: C74S

DomainStartEndE-ValueType
low complexity region 71 94 N/A INTRINSIC
LIM 98 151 7.34e-13 SMART
LIM 159 213 3.17e-17 SMART
HOX 248 310 1.1e-23 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137436
Predicted Effect probably benign
Transcript: ENSMUST00000148852
AA Change: C45S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: C45S

DomainStartEndE-ValueType
low complexity region 42 65 N/A INTRINSIC
LIM 69 122 7.34e-13 SMART
LIM 130 184 3.17e-17 SMART
HOX 219 281 1.1e-23 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187180
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 protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]
PHENOTYPE: Homozygous mutation of this gene results in impaired migration and specification of cortical interneurons, postnatal lethality and weakness. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ap3m2 T A 8: 23,289,663 (GRCm39) I147F probably benign Het
Areg T A 5: 91,288,954 (GRCm39) S87T probably damaging Het
Arid1b T A 17: 5,369,133 (GRCm39) probably benign Het
Arl6ip6 A G 2: 53,082,156 (GRCm39) R8G probably benign Het
Brms1 A G 19: 5,096,723 (GRCm39) E135G possibly damaging Het
Ccser1 A G 6: 61,615,505 (GRCm39) probably benign Het
Dock3 A T 9: 106,784,433 (GRCm39) M258K possibly damaging Het
Epb41l4a T G 18: 33,934,678 (GRCm39) D562A possibly damaging Het
Etaa1 G A 11: 17,896,005 (GRCm39) T704I probably damaging Het
Fer1l4 T A 2: 155,878,376 (GRCm39) H972L probably damaging Het
Foxn1 A G 11: 78,252,320 (GRCm39) M356T probably damaging Het
Gfral C A 9: 76,072,107 (GRCm39) G388* probably null Het
Gm12258 A G 11: 58,739,520 (GRCm39) T3A probably benign Het
Hoxa5 T C 6: 52,181,311 (GRCm39) N7S probably damaging Het
Itgb4 T C 11: 115,881,746 (GRCm39) L765P probably damaging Het
Jchain C T 5: 88,669,383 (GRCm39) C90Y probably damaging Het
Klhl40 A G 9: 121,607,983 (GRCm39) Y381C probably damaging Het
Magel2 A G 7: 62,030,632 (GRCm39) S1179G unknown Het
Mapre3 T C 5: 31,022,241 (GRCm39) I236T probably damaging Het
Mcf2l A T 8: 13,064,010 (GRCm39) probably null Het
Med13 A T 11: 86,219,323 (GRCm39) H374Q probably benign Het
Meioc A G 11: 102,565,113 (GRCm39) Y187C probably benign Het
Myh1 G A 11: 67,108,689 (GRCm39) M1368I probably benign Het
Or14a258 A T 7: 86,035,208 (GRCm39) I220N possibly damaging Het
Or8b54 A G 9: 38,686,826 (GRCm39) I92V probably damaging Het
Phrf1 T C 7: 140,842,394 (GRCm39) Y1501H probably damaging Het
Pigb T C 9: 72,929,573 (GRCm39) T337A probably damaging Het
Pls1 T C 9: 95,655,751 (GRCm39) K334E probably benign Het
Pramel51 C T 12: 88,145,225 (GRCm39) V34I possibly damaging Het
Rab3b T C 4: 108,797,999 (GRCm39) C226R probably damaging Het
Ryr2 A T 13: 11,571,571 (GRCm39) I4889N possibly damaging Het
Serpinb1a G A 13: 33,029,398 (GRCm39) S210L probably benign Het
Slc52a3 A G 2: 151,849,522 (GRCm39) I390V probably benign Het
Slc6a7 C A 18: 61,136,382 (GRCm39) A340S probably damaging Het
Tcaf3 T C 6: 42,570,615 (GRCm39) Y379C probably damaging Het
Tex261 A G 6: 83,748,222 (GRCm39) V180A probably benign Het
Tnnt1 C T 7: 4,517,211 (GRCm39) probably null Het
Ttn T C 2: 76,798,847 (GRCm39) T476A possibly damaging Het
Vcan A G 13: 89,852,288 (GRCm39) S891P probably benign Het
Vmn2r16 T A 5: 109,511,627 (GRCm39) D611E possibly damaging Het
Vmn2r68 T C 7: 84,886,819 (GRCm39) T32A probably benign Het
Vwde T G 6: 13,190,526 (GRCm39) S522R probably benign Het
Wdr3 G A 3: 100,054,105 (GRCm39) probably benign Het
Wfs1 G T 5: 37,128,907 (GRCm39) Q288K probably benign Het
Zfp142 A G 1: 74,618,699 (GRCm39) V120A probably damaging Het
Zfp672 A G 11: 58,208,192 (GRCm39) F43S probably damaging Het
Znhit3 A T 11: 84,802,283 (GRCm39) probably benign Het
Other mutations in Lhx6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00088:Lhx6 APN 2 35,981,728 (GRCm39) splice site probably benign
IGL01413:Lhx6 APN 2 35,993,528 (GRCm39) missense probably benign 0.24
IGL03154:Lhx6 APN 2 35,984,455 (GRCm39) splice site probably null
R1546:Lhx6 UTSW 2 35,981,049 (GRCm39) missense probably benign 0.00
R1630:Lhx6 UTSW 2 35,992,913 (GRCm39) missense probably damaging 1.00
R1785:Lhx6 UTSW 2 35,977,470 (GRCm39) nonsense probably null
R1786:Lhx6 UTSW 2 35,977,470 (GRCm39) nonsense probably null
R1792:Lhx6 UTSW 2 35,977,387 (GRCm39) missense probably damaging 1.00
R2126:Lhx6 UTSW 2 35,981,336 (GRCm39) missense possibly damaging 0.94
R2145:Lhx6 UTSW 2 35,977,478 (GRCm39) missense probably benign 0.01
R2167:Lhx6 UTSW 2 35,993,371 (GRCm39) missense probably damaging 1.00
R2393:Lhx6 UTSW 2 35,981,402 (GRCm39) missense probably benign 0.22
R5102:Lhx6 UTSW 2 35,984,222 (GRCm39) splice site probably null
R5418:Lhx6 UTSW 2 35,977,378 (GRCm39) critical splice donor site probably null
R6735:Lhx6 UTSW 2 35,981,390 (GRCm39) missense probably damaging 0.99
R7462:Lhx6 UTSW 2 35,974,083 (GRCm39) missense possibly damaging 0.86
R7546:Lhx6 UTSW 2 35,993,357 (GRCm39) critical splice donor site probably null
R8870:Lhx6 UTSW 2 35,995,232 (GRCm39) unclassified probably benign
R9192:Lhx6 UTSW 2 35,981,145 (GRCm39) missense probably benign 0.10
R9667:Lhx6 UTSW 2 35,980,979 (GRCm39) missense possibly damaging 0.93
Posted On 2013-11-05