Incidental Mutation 'R7462:Lhx6'
ID 578485
Institutional Source Beutler Lab
Gene Symbol Lhx6
Ensembl Gene ENSMUSG00000026890
Gene Name LIM homeobox protein 6
Synonyms
MMRRC Submission 045536-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.930) question?
Stock # R7462 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 35971965-35995420 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 35974083 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 359 (I359T)
Ref Sequence ENSEMBL: ENSMUSP00000108585 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028256] [ENSMUST00000112960] [ENSMUST00000112961] [ENSMUST00000112963] [ENSMUST00000112966] [ENSMUST00000112967] [ENSMUST00000136821] [ENSMUST00000148852]
AlphaFold Q9R1R0
Predicted Effect probably benign
Transcript: ENSMUST00000028256
SMART Domains Protein: ENSMUSP00000028256
Gene: ENSMUSG00000026894

DomainStartEndE-ValueType
MORN 6 27 1.24e1 SMART
MORN 29 50 3.61e-2 SMART
Pfam:MORN 54 75 2e-4 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000112960
AA Change: I388T

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: I388T

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 possibly damaging
Transcript: ENSMUST00000112961
AA Change: I359T

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: I359T

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 possibly damaging
Transcript: ENSMUST00000112963
AA Change: I359T

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: I359T

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

DomainStartEndE-ValueType
LIM 10 64 3.17e-17 SMART
Predicted Effect silent
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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 98% (60/61)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ank2 G C 3: 126,736,683 (GRCm39) T3067S unknown Het
Ankrd28 T C 14: 31,500,886 (GRCm39) N35S probably benign Het
Bicra A T 7: 15,713,060 (GRCm39) S996T possibly damaging Het
Btbd7 T C 12: 102,803,981 (GRCm39) E353G possibly damaging Het
Cdhr2 A T 13: 54,874,552 (GRCm39) I875F probably damaging Het
Ceacam5 A T 7: 17,494,764 (GRCm39) Y924F probably damaging Het
Clca4b A G 3: 144,628,621 (GRCm39) I362T probably benign Het
Dchs2 A G 3: 83,253,462 (GRCm39) probably null Het
Dlc1 T A 8: 37,405,118 (GRCm39) T224S unknown Het
Dmxl2 T C 9: 54,273,916 (GRCm39) probably null Het
Dnajc1 A G 2: 18,313,710 (GRCm39) F137S probably damaging Het
E130311K13Rik T C 3: 63,836,722 (GRCm39) T24A probably benign Het
Eya1 T C 1: 14,301,638 (GRCm39) E317G probably null Het
Fpr-rs6 A G 17: 20,402,485 (GRCm39) L292P probably damaging Het
Gca G T 2: 62,502,753 (GRCm39) D54Y possibly damaging Het
Gm45861 G A 8: 28,024,517 (GRCm39) probably null Het
Gm57858 T A 3: 36,080,055 (GRCm39) probably null Het
Gtf2a1l A G 17: 89,001,566 (GRCm39) T141A possibly damaging Het
Hgsnat T C 8: 26,447,241 (GRCm39) N351S probably benign Het
Htr1f A T 16: 64,746,383 (GRCm39) V303E probably damaging Het
Iars2 C A 1: 185,055,063 (GRCm39) W302L probably damaging Het
Igkv4-74 T A 6: 69,162,100 (GRCm39) Q23L possibly damaging Het
Il18 A T 9: 50,476,673 (GRCm39) probably benign Het
Ints4 A G 7: 97,155,335 (GRCm39) D329G probably benign Het
Itsn1 T C 16: 91,650,073 (GRCm39) F249S possibly damaging Het
Ktn1 A G 14: 47,932,089 (GRCm39) E672G probably null Het
Lrp1b T C 2: 41,003,041 (GRCm39) E2030G Het
Macf1 T A 4: 123,386,556 (GRCm39) K1114N probably damaging Het
Mbd5 A G 2: 49,147,892 (GRCm39) M701V possibly damaging Het
Mcemp1 A T 8: 3,717,065 (GRCm39) M69L probably benign Het
Mfsd4b2 T A 10: 39,797,877 (GRCm39) K159N probably benign Het
Mroh2b T A 15: 4,938,109 (GRCm39) D243E probably damaging Het
Muc21 T C 17: 35,931,568 (GRCm39) S873G unknown Het
Mug1 A T 6: 121,852,399 (GRCm39) Q829L probably benign Het
Nav3 A T 10: 109,659,439 (GRCm39) V726E probably damaging Het
Nfib T C 4: 82,271,826 (GRCm39) Q247R probably benign Het
Npbwr1 T C 1: 5,987,151 (GRCm39) N121S probably damaging Het
Or1e19 T C 11: 73,316,296 (GRCm39) D171G probably benign Het
Or52b2 T A 7: 104,986,707 (GRCm39) D72V probably damaging Het
Or5h19 A T 16: 58,856,379 (GRCm39) C240* probably null Het
Pkd1l3 A G 8: 110,355,409 (GRCm39) S726G probably benign Het
Ppip5k1 A T 2: 121,167,232 (GRCm39) V847D probably damaging Het
Ptpn18 G A 1: 34,512,445 (GRCm39) D417N possibly damaging Het
Ripor2 G A 13: 24,880,290 (GRCm39) V385M unknown Het
Rufy1 C T 11: 50,298,655 (GRCm39) V379M possibly damaging Het
S100a5 A G 3: 90,517,207 (GRCm39) K26R probably damaging Het
Sin3a T C 9: 57,002,809 (GRCm39) S234P probably benign Het
Sirt7 G A 11: 120,511,618 (GRCm39) T225I probably benign Het
Slc34a1 A T 13: 24,006,401 (GRCm39) T476S probably damaging Het
Slc38a6 T A 12: 73,397,351 (GRCm39) M331K probably benign Het
Spam1 T C 6: 24,796,907 (GRCm39) I286T probably damaging Het
Syne1 T A 10: 5,002,793 (GRCm39) I214F possibly damaging Het
Tmtc1 A G 6: 148,226,643 (GRCm39) L427P probably damaging Het
Tpbg G A 9: 85,726,903 (GRCm39) A291T possibly damaging Het
Zfp40 A G 17: 23,397,362 (GRCm39) F45S possibly damaging Het
Zfp451 C T 1: 33,816,094 (GRCm39) V619M probably damaging Het
Zim1 A G 7: 6,680,811 (GRCm39) L284P probably damaging Het
Zkscan4 A G 13: 21,668,044 (GRCm39) E165G probably benign Het
Zmynd11 T A 13: 9,748,720 (GRCm39) N154Y probably benign Het
Zscan12 A T 13: 21,553,457 (GRCm39) H427L possibly damaging Het
Other mutations in Lhx6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00088:Lhx6 APN 2 35,981,728 (GRCm39) splice site probably benign
IGL01391:Lhx6 APN 2 35,993,477 (GRCm39) missense probably benign 0.00
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
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
Predicted Primers PCR Primer
(F):5'- GATGCCACATTTCAGGGAGC -3'
(R):5'- CTGCTCTTGCTATGAGAGATCAC -3'

Sequencing Primer
(F):5'- GACTCTGCTGCTCCTGGTG -3'
(R):5'- TTTACACATGAGGAAACAGGCTTG -3'
Posted On 2019-10-07