Incidental Mutation 'R5102:Lhx6'
ID392398
Institutional Source Beutler Lab
Gene Symbol Lhx6
Ensembl Gene ENSMUSG00000026890
Gene NameLIM homeobox protein 6
Synonyms
MMRRC Submission 042690-MU
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.898) question?
Stock #R5102 (G1)
Quality Score225
Status Not validated
Chromosome2
Chromosomal Location36081953-36105408 bp(-) (GRCm38)
Type of Mutationsplice site (3 bp from exon)
DNA Base Change (assembly) T to C at 36094210 bp
ZygosityHeterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000135693 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000112960] [ENSMUST00000112960] [ENSMUST00000112961] [ENSMUST00000112961] [ENSMUST00000112963] [ENSMUST00000112963] [ENSMUST00000112966] [ENSMUST00000112966] [ENSMUST00000112967] [ENSMUST00000112967] [ENSMUST00000136821] [ENSMUST00000148852] [ENSMUST00000148852]
Predicted Effect probably null
Transcript: ENSMUST00000112960
SMART Domains Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112960
SMART Domains Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112961
SMART Domains Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112961
SMART Domains Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112963
SMART Domains Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112963
SMART Domains Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112966
SMART Domains Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112966
SMART Domains Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112967
SMART Domains Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000112967
SMART Domains Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000136821
SMART Domains Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890

DomainStartEndE-ValueType
LIM 10 64 3.17e-17 SMART
Predicted Effect probably null
Transcript: ENSMUST00000148852
SMART Domains Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890

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 null
Transcript: ENSMUST00000148852
SMART Domains Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890

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
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 91.3%
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2810006K23Rik A G 5: 124,338,891 N83D probably damaging Het
Aox4 C T 1: 58,240,778 R518C probably damaging Het
Apbb2 A T 5: 66,312,249 probably null Het
Arhgap45 C T 10: 80,021,428 P254S probably benign Het
Arl4c T C 1: 88,701,600 D22G probably damaging Het
Asxl1 A G 2: 153,400,955 T1142A probably benign Het
BC035044 T C 6: 128,884,986 probably benign Het
Bmp4 T C 14: 46,384,001 N362S probably damaging Het
Cbll1 G T 12: 31,487,913 T280N probably damaging Het
Cdh10 A T 15: 18,986,885 T401S probably benign Het
Cps1 A T 1: 67,206,793 M1148L probably benign Het
Crybg1 T C 10: 43,997,836 D1092G probably damaging Het
Cyth2 A G 7: 45,810,702 S173P probably damaging Het
D3Ertd254e G A 3: 36,162,665 C55Y possibly damaging Het
D6Ertd527e A T 6: 87,111,811 I319F unknown Het
Dchs1 A T 7: 105,772,177 H345Q probably benign Het
Ddx50 A T 10: 62,640,861 V211E probably damaging Het
Dlx6 AGG AG 6: 6,865,180 probably null Het
Dnajb5 G A 4: 42,956,639 D109N possibly damaging Het
Dner A T 1: 84,405,970 N564K probably damaging Het
Fam234b T C 6: 135,209,284 S97P probably benign Het
Fam53b G A 7: 132,715,955 R60* probably null Het
Fmo3 T G 1: 162,963,977 K244Q probably benign Het
Gm12800 T C 4: 101,909,239 F40S probably damaging Het
Golim4 A G 3: 75,903,272 I192T possibly damaging Het
Gpr1 A G 1: 63,183,167 V303A probably damaging Het
Gprin1 T C 13: 54,739,763 M233V probably benign Het
Gtf2f1 A T 17: 57,003,626 V443D probably damaging Het
H2afy C G 13: 56,096,123 probably null Het
Hmgcs2 T C 3: 98,280,470 probably benign Het
Ide T A 19: 37,314,984 I271L unknown Het
Kat8 G A 7: 127,924,816 E343K probably damaging Het
Kif14 A G 1: 136,516,403 I1378V probably benign Het
Lhx3 TCCTACGGGCCGGCCC TCC 2: 26,201,423 probably null Het
Lrp2 C T 2: 69,489,158 G2007D probably damaging Het
Lrp5 T C 19: 3,659,304 K142R probably damaging Het
Mrpl2 G A 17: 46,650,038 R286Q probably benign Het
Nacad T A 11: 6,598,528 D1402V probably damaging Het
Ndfip2 T C 14: 105,298,105 I275T possibly damaging Het
Neb A C 2: 52,226,570 V4131G possibly damaging Het
Nfe2l1 G A 11: 96,822,108 A83V probably damaging Het
Nos3 A G 5: 24,371,627 D418G probably damaging Het
Olfr1126 A T 2: 87,457,794 M210L probably benign Het
Olfr353 T A 2: 36,890,044 K268M possibly damaging Het
Plcd4 A G 1: 74,565,154 T764A probably damaging Het
Plppr3 G T 10: 79,865,386 P541T possibly damaging Het
Polr2a A G 11: 69,746,945 I191T possibly damaging Het
Rab11fip1 T C 8: 27,156,374 K225E probably damaging Het
Rara A T 11: 98,966,359 Q64L possibly damaging Het
Rtkn G A 6: 83,149,773 V305M probably damaging Het
Sh2b1 A C 7: 126,471,236 F399V probably benign Het
Slc7a4 T C 16: 17,575,618 T106A probably damaging Het
Srcap G A 7: 127,530,623 G539D probably damaging Het
Stab1 C T 14: 31,148,017 probably null Het
Other mutations in Lhx6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00088:Lhx6 APN 2 36091716 splice site probably benign
IGL01391:Lhx6 APN 2 36103465 missense probably benign 0.00
IGL01413:Lhx6 APN 2 36103516 missense probably benign 0.24
IGL03154:Lhx6 APN 2 36094443 splice site probably null
R1546:Lhx6 UTSW 2 36091037 missense probably benign 0.00
R1630:Lhx6 UTSW 2 36102901 missense probably damaging 1.00
R1785:Lhx6 UTSW 2 36087458 nonsense probably null
R1786:Lhx6 UTSW 2 36087458 nonsense probably null
R1792:Lhx6 UTSW 2 36087375 missense probably damaging 1.00
R2126:Lhx6 UTSW 2 36091324 missense possibly damaging 0.94
R2145:Lhx6 UTSW 2 36087466 missense probably benign 0.01
R2167:Lhx6 UTSW 2 36103359 missense probably damaging 1.00
R2393:Lhx6 UTSW 2 36091390 missense probably benign 0.22
R5418:Lhx6 UTSW 2 36087366 critical splice donor site probably null
R6735:Lhx6 UTSW 2 36091378 missense probably damaging 0.99
R7462:Lhx6 UTSW 2 36084071 missense possibly damaging 0.86
R7546:Lhx6 UTSW 2 36103345 critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TAGCCCATGCAAATGATGGAGC -3'
(R):5'- GCAGCCGATTTGGAACCAAG -3'

Sequencing Primer
(F):5'- AGCCAGAGCGCATGTTC -3'
(R):5'- ATTTGGAACCAAGTGCGCC -3'
Posted On2016-06-15