Incidental Mutation 'R6852:Lhx9'
ID 534995
Institutional Source Beutler Lab
Gene Symbol Lhx9
Ensembl Gene ENSMUSG00000019230
Gene Name LIM homeobox protein 9
Synonyms 3110009O07Rik, Lhx9 alpha, LH2B
MMRRC Submission 045023-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.787) question?
Stock # R6852 (G1)
Quality Score 217.468
Status Not validated
Chromosome 1
Chromosomal Location 138752924-138776315 bp(-) (GRCm39)
Type of Mutation frame shift
DNA Base Change (assembly) ACC to ACCC at 138769544 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000142268 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019374] [ENSMUST00000046870] [ENSMUST00000093486] [ENSMUST00000112026] [ENSMUST00000112030] [ENSMUST00000194557]
AlphaFold Q9WUH2
Predicted Effect probably null
Transcript: ENSMUST00000019374
SMART Domains Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230

DomainStartEndE-ValueType
LIM 70 123 4.48e-17 SMART
LIM 132 186 8.04e-19 SMART
HOX 267 319 1.89e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000046870
SMART Domains Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230

DomainStartEndE-ValueType
LIM 61 114 4.48e-17 SMART
LIM 123 177 8.04e-19 SMART
HOX 258 320 8.07e-22 SMART
low complexity region 344 368 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000093486
SMART Domains Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230

DomainStartEndE-ValueType
LIM 61 114 4.48e-17 SMART
LIM 123 177 8.04e-19 SMART
HOX 258 310 1.89e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000112026
SMART Domains Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230

DomainStartEndE-ValueType
LIM 70 123 4.48e-17 SMART
LIM 132 186 8.04e-19 SMART
HOX 267 329 8.07e-22 SMART
low complexity region 353 377 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000112030
SMART Domains Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230

DomainStartEndE-ValueType
LIM 61 114 4.48e-17 SMART
LIM 123 177 8.04e-19 SMART
HOX 258 310 1.89e-4 SMART
Predicted Effect probably null
Transcript: ENSMUST00000194557
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
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 the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failed proliferation of the somatic cells of the genital ridge resulting in lack of discrete gonad formation, infertility in both sexes, and female-like genitalia in genetically male mice. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik C T 3: 137,770,930 (GRCm39) Q40* probably null Het
1700034E13Rik T C 18: 52,796,705 (GRCm39) V81A probably damaging Het
A630089N07Rik A G 16: 97,866,855 (GRCm39) I369T probably benign Het
Aatk T A 11: 119,901,294 (GRCm39) Q977L probably benign Het
Abca4 A T 3: 121,928,844 (GRCm39) Q144H probably damaging Het
Ampd3 T C 7: 110,401,753 (GRCm39) F416L probably benign Het
Anks1b A G 10: 90,096,516 (GRCm39) E425G probably damaging Het
Atm A G 9: 53,393,730 (GRCm39) S1737P possibly damaging Het
Bsph1 T A 7: 13,204,255 (GRCm39) probably null Het
Cabyr C T 18: 12,887,154 (GRCm39) P262S probably benign Het
Cdc14a G A 3: 116,122,325 (GRCm39) P214L possibly damaging Het
Cep128 C A 12: 91,333,116 (GRCm39) probably null Het
Cfh T A 1: 140,075,487 (GRCm39) R250S probably damaging Het
Ddx39a T C 8: 84,449,646 (GRCm39) I417T probably benign Het
Dgka T A 10: 128,558,408 (GRCm39) K548M probably damaging Het
Efr3a G A 15: 65,701,679 (GRCm39) V198I probably benign Het
Elapor1 T C 3: 108,389,654 (GRCm39) E203G probably damaging Het
Epg5 C T 18: 78,056,106 (GRCm39) T1760I probably damaging Het
Fat1 T C 8: 45,488,635 (GRCm39) V3472A possibly damaging Het
Fbxo48 T A 11: 16,903,402 (GRCm39) N9K probably benign Het
Fcgbpl1 T A 7: 27,846,560 (GRCm39) I1084N probably damaging Het
Fer1l6 A T 15: 58,466,727 (GRCm39) H833L probably damaging Het
Foxn1 G T 11: 78,251,786 (GRCm39) Q482K probably benign Het
Fstl5 A G 3: 76,615,162 (GRCm39) D741G probably damaging Het
Gmip C T 8: 70,270,641 (GRCm39) Q55* probably null Het
H2-T5 T C 17: 36,478,965 (GRCm39) N95D possibly damaging Het
Hapln2 G A 3: 87,929,958 (GRCm39) T306M possibly damaging Het
Kat6a T A 8: 23,428,676 (GRCm39) S1344T probably benign Het
Kctd1 C T 18: 15,119,401 (GRCm39) D705N possibly damaging Het
Micall2 G T 5: 139,701,548 (GRCm39) A482D possibly damaging Het
Mindy3 T A 2: 12,424,063 (GRCm39) M1L possibly damaging Het
Mtdh A G 15: 34,136,867 (GRCm39) E352G probably damaging Het
Muc5ac G A 7: 141,370,644 (GRCm39) V3219I probably benign Het
Myh4 A G 11: 67,143,794 (GRCm39) probably null Het
Ncor1 A G 11: 62,234,071 (GRCm39) I377T probably damaging Het
Oog4 C A 4: 143,165,679 (GRCm39) C156F possibly damaging Het
Or5m9 A T 2: 85,876,948 (GRCm39) I41F probably benign Het
Pcyt1a T C 16: 32,288,938 (GRCm39) S260P probably damaging Het
Phf3 A T 1: 30,843,711 (GRCm39) F1749L probably damaging Het
Prickle2 T C 6: 92,353,525 (GRCm39) D647G probably benign Het
Raver2 T C 4: 100,990,787 (GRCm39) S387P probably benign Het
Relch T C 1: 105,681,320 (GRCm39) L1184P probably damaging Het
Rgs19 A G 2: 181,330,941 (GRCm39) S231P possibly damaging Het
Rpl8 G T 15: 76,790,149 (GRCm39) R198L probably benign Het
Sacs T A 14: 61,416,737 (GRCm39) S77T possibly damaging Het
Samd14 G A 11: 94,912,280 (GRCm39) G219D probably damaging Het
Sec16a C T 2: 26,331,431 (GRCm39) V195M probably damaging Het
Sesn2 C T 4: 132,221,113 (GRCm39) V453I possibly damaging Het
Slc46a3 A T 5: 147,822,970 (GRCm39) C291S probably damaging Het
Smarcal1 A G 1: 72,630,332 (GRCm39) T129A possibly damaging Het
Sorl1 T A 9: 41,935,694 (GRCm39) R1041W possibly damaging Het
Sptlc3 T C 2: 139,408,506 (GRCm39) I207T probably benign Het
Srgap3 T C 6: 112,793,622 (GRCm39) D118G probably damaging Het
Tas2r117 T A 6: 132,779,892 (GRCm39) V10D probably benign Het
Tbcd A G 11: 121,500,206 (GRCm39) K1111E probably benign Het
Tor1aip1 A T 1: 155,911,566 (GRCm39) L139Q probably damaging Het
Trbv23 T C 6: 41,193,181 (GRCm39) V23A probably damaging Het
Ttll3 AAGTA AAGTATAGTA 6: 113,376,120 (GRCm39) probably null Het
Ttll3 GGCAAAG GGCAAAGCAAAG 6: 113,376,116 (GRCm39) probably null Het
Ttll3 CAAAGTAA CAAAGTAAAGTAA 6: 113,376,118 (GRCm39) probably null Het
Vmn1r42 T G 6: 89,821,769 (GRCm39) T267P possibly damaging Het
Vmn2r53 C A 7: 12,340,441 (GRCm39) V11F probably damaging Het
Vmn2r67 T C 7: 84,801,361 (GRCm39) M192V probably damaging Het
Vmn2r78 T C 7: 86,603,811 (GRCm39) V663A probably damaging Het
Zdhhc1 C T 8: 106,203,704 (GRCm39) G156S possibly damaging Het
Zfp318 AGAAG AGAAGAGGAAG 17: 46,723,464 (GRCm39) probably benign Het
Zfp318 GAAGAA GAAGAAAAAGAA 17: 46,723,459 (GRCm39) probably benign Het
Zfp318 AAGAAG AAGAAGTAGAAG 17: 46,723,460 (GRCm39) probably benign Het
Zfp560 A G 9: 20,259,339 (GRCm39) C508R probably damaging Het
Zfp654 G A 16: 64,606,961 (GRCm39) L414F probably damaging Het
Zfp872 A T 9: 22,111,355 (GRCm39) Y278F probably damaging Het
Zscan20 T C 4: 128,483,515 (GRCm39) S385G probably damaging Het
Other mutations in Lhx9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00955:Lhx9 APN 1 138,756,418 (GRCm39) missense possibly damaging 0.74
IGL01624:Lhx9 APN 1 138,760,521 (GRCm39) nonsense probably null
IGL02149:Lhx9 APN 1 138,759,172 (GRCm39) missense probably damaging 1.00
IGL02452:Lhx9 APN 1 138,769,580 (GRCm39) missense probably damaging 1.00
IGL02982:Lhx9 APN 1 138,766,349 (GRCm39) missense probably damaging 1.00
R0123:Lhx9 UTSW 1 138,766,417 (GRCm39) missense probably damaging 1.00
R0134:Lhx9 UTSW 1 138,766,417 (GRCm39) missense probably damaging 1.00
R0141:Lhx9 UTSW 1 138,767,744 (GRCm39) missense possibly damaging 0.86
R0225:Lhx9 UTSW 1 138,766,417 (GRCm39) missense probably damaging 1.00
R0281:Lhx9 UTSW 1 138,760,642 (GRCm39) missense probably benign 0.00
R1460:Lhx9 UTSW 1 138,766,447 (GRCm39) splice site probably benign
R1932:Lhx9 UTSW 1 138,769,747 (GRCm39) start gained probably benign
R4738:Lhx9 UTSW 1 138,760,486 (GRCm39) missense probably damaging 1.00
R4792:Lhx9 UTSW 1 138,766,089 (GRCm39) missense possibly damaging 0.87
R4820:Lhx9 UTSW 1 138,766,105 (GRCm39) missense probably benign 0.00
R4877:Lhx9 UTSW 1 138,766,092 (GRCm39) missense probably benign 0.04
R6035:Lhx9 UTSW 1 138,766,281 (GRCm39) missense possibly damaging 0.67
R6035:Lhx9 UTSW 1 138,766,281 (GRCm39) missense possibly damaging 0.67
R6825:Lhx9 UTSW 1 138,769,544 (GRCm39) frame shift probably null
R6853:Lhx9 UTSW 1 138,769,544 (GRCm39) frame shift probably null
R7264:Lhx9 UTSW 1 138,760,489 (GRCm39) missense probably damaging 0.98
R8097:Lhx9 UTSW 1 138,766,089 (GRCm39) missense probably damaging 0.97
R8164:Lhx9 UTSW 1 138,760,518 (GRCm39) missense probably damaging 1.00
R8245:Lhx9 UTSW 1 138,766,179 (GRCm39) missense probably benign 0.24
R8278:Lhx9 UTSW 1 138,766,324 (GRCm39) missense probably damaging 0.98
R8951:Lhx9 UTSW 1 138,769,704 (GRCm39) missense probably damaging 1.00
R9761:Lhx9 UTSW 1 138,774,934 (GRCm39) missense probably benign 0.09
Z1177:Lhx9 UTSW 1 138,759,236 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- AGACTGGAGAGCTCAGGACTAC -3'
(R):5'- TCACTCGAATGAACTGAGAGC -3'

Sequencing Primer
(F):5'- GAGAGCTCAGGACTACAACATCTTAG -3'
(R):5'- TCGAATGAACTGAGAGCCCCAG -3'
Posted On 2018-09-12