Incidental Mutation 'R4738:Lhx9'
ID 359391
Institutional Source Beutler Lab
Gene Symbol Lhx9
Ensembl Gene ENSMUSG00000019230
Gene Name LIM homeobox protein 9
Synonyms 3110009O07Rik, Lhx9 alpha, LH2B
MMRRC Submission 041964-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.787) question?
Stock # R4738 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 138752924-138776315 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 138760486 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 288 (L288P)
Ref Sequence ENSEMBL: ENSMUSP00000107661 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019374] [ENSMUST00000046870] [ENSMUST00000093486] [ENSMUST00000112026] [ENSMUST00000112030] [ENSMUST00000194557]
AlphaFold Q9WUH2
Predicted Effect probably damaging
Transcript: ENSMUST00000019374
AA Change: L297P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: L297P

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 damaging
Transcript: ENSMUST00000046870
AA Change: L288P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: L288P

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 damaging
Transcript: ENSMUST00000093486
AA Change: L288P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: L288P

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 damaging
Transcript: ENSMUST00000112026
AA Change: L297P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: L297P

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 damaging
Transcript: ENSMUST00000112030
AA Change: L288P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: L288P

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 noncoding transcript
Transcript: ENSMUST00000192425
Predicted Effect probably benign
Transcript: ENSMUST00000194557
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.9%
  • 20x: 94.3%
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 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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg3 A G 5: 105,121,849 (GRCm39) I176T probably benign Het
Abtb3 C T 10: 85,463,112 (GRCm39) Q626* probably null Het
Angpt2 C T 8: 18,791,075 (GRCm39) D74N probably benign Het
Apol10a C T 15: 77,372,841 (GRCm39) T159I possibly damaging Het
Areg T C 5: 91,294,583 (GRCm39) I247T possibly damaging Het
Atg16l2 A G 7: 100,946,385 (GRCm39) L129P probably damaging Het
Atp6v1b2 T A 8: 69,556,062 (GRCm39) S246T probably benign Het
Atp8b1 T C 18: 64,678,251 (GRCm39) R882G probably benign Het
Atp9a A G 2: 168,510,101 (GRCm39) V444A probably benign Het
Babam2 T A 5: 32,058,486 (GRCm39) Y211N probably damaging Het
Ccdc127 T G 13: 74,505,187 (GRCm39) probably benign Het
Cep192 A T 18: 68,017,901 (GRCm39) K2500* probably null Het
Cnot4 T C 6: 35,028,311 (GRCm39) N435S probably benign Het
Col12a1 T C 9: 79,606,564 (GRCm39) I620V probably damaging Het
Cyth4 G A 15: 78,490,074 (GRCm39) M62I probably benign Het
Dbt T C 3: 116,332,781 (GRCm39) I200T probably damaging Het
Dchs1 C T 7: 105,407,880 (GRCm39) R1984Q probably damaging Het
Depdc5 A G 5: 33,132,666 (GRCm39) M1237V probably benign Het
Disp2 A G 2: 118,620,807 (GRCm39) Y513C probably damaging Het
Dph7 T C 2: 24,853,143 (GRCm39) S86P possibly damaging Het
Eif3b T A 5: 140,415,833 (GRCm39) M384K probably benign Het
Emc1 G T 4: 139,089,513 (GRCm39) G227V possibly damaging Het
Eri2 A G 7: 119,386,955 (GRCm39) probably null Het
Frzb A G 2: 80,254,941 (GRCm39) probably null Het
Ganc T A 2: 120,283,075 (GRCm39) V743D probably damaging Het
Gfpt1 C A 6: 87,031,729 (GRCm39) probably benign Het
Gm3086 A T 12: 70,016,155 (GRCm39) probably benign Het
Gsdmc2 A T 15: 63,698,650 (GRCm39) Y315* probably null Het
Haus6 A G 4: 86,518,986 (GRCm39) probably null Het
Hhip C T 8: 80,719,199 (GRCm39) D443N probably damaging Het
Isg15 T C 4: 156,284,319 (GRCm39) M70V probably benign Het
Kank2 T C 9: 21,685,915 (GRCm39) N653S probably damaging Het
Klhdc1 G T 12: 69,329,907 (GRCm39) R345S probably benign Het
Larp7 A G 3: 127,339,694 (GRCm39) probably null Het
Lgals12 A G 19: 7,581,464 (GRCm39) V81A probably benign Het
Mcpt9 T A 14: 56,264,456 (GRCm39) H213L probably damaging Het
Met T C 6: 17,491,540 (GRCm39) C101R probably damaging Het
Myo16 G T 8: 10,423,527 (GRCm39) G288W probably damaging Het
Neb A C 2: 52,077,494 (GRCm39) S1846A probably damaging Het
Nr3c2 T C 8: 77,635,936 (GRCm39) S346P possibly damaging Het
Obi1 C T 14: 104,747,819 (GRCm39) D43N probably damaging Het
Or10h5 A G 17: 33,434,784 (GRCm39) F178S probably benign Het
Or1e1c G T 11: 73,266,176 (GRCm39) L200F possibly damaging Het
Or51e1 T A 7: 102,359,378 (GRCm39) I304N probably damaging Het
Or5h19 T C 16: 58,856,558 (GRCm39) I181V probably benign Het
Or5p63 A T 7: 107,811,201 (GRCm39) N178K probably damaging Het
Osbpl10 A G 9: 115,045,642 (GRCm39) E426G probably damaging Het
Ovgp1 T C 3: 105,887,234 (GRCm39) V210A probably damaging Het
Pam A T 1: 97,850,857 (GRCm39) V167D probably damaging Het
Pappa2 T C 1: 158,784,582 (GRCm39) R143G probably benign Het
Pbx4 C T 8: 70,317,619 (GRCm39) T201M probably damaging Het
Pcdhb9 T C 18: 37,536,468 (GRCm39) C821R probably benign Het
Plekhg3 T C 12: 76,623,688 (GRCm39) I976T probably damaging Het
Pold1 G A 7: 44,190,753 (GRCm39) R304C probably damaging Het
Prss38 T C 11: 59,263,771 (GRCm39) T314A probably benign Het
Psph T C 5: 129,846,450 (GRCm39) probably null Het
Ptprj G A 2: 90,270,987 (GRCm39) P1247L probably damaging Het
Rab3gap1 A G 1: 127,862,173 (GRCm39) E648G probably damaging Het
Ralgds A G 2: 28,435,428 (GRCm39) E465G probably damaging Het
Rfng T C 11: 120,674,790 (GRCm39) T67A probably damaging Het
Rps6kl1 G T 12: 85,187,161 (GRCm39) F181L probably benign Het
Spata46 G A 1: 170,139,455 (GRCm39) M151I possibly damaging Het
Ssbp1 T A 6: 40,454,914 (GRCm39) N124K probably damaging Het
Sspo C T 6: 48,455,330 (GRCm39) A3064V possibly damaging Het
Tbc1d8 G A 1: 39,441,959 (GRCm39) T211I possibly damaging Het
Tdpoz4 T C 3: 93,704,396 (GRCm39) I231T probably damaging Het
Tff3 G A 17: 31,346,483 (GRCm39) P30S probably benign Het
Thg1l C T 11: 45,845,018 (GRCm39) R18Q probably damaging Het
Tlk2 T A 11: 105,147,708 (GRCm39) H369Q probably benign Het
Tnfaip8 A G 18: 50,223,569 (GRCm39) T14A probably damaging Het
Tspan17 T A 13: 54,942,877 (GRCm39) C116* probably null Het
Ttn T C 2: 76,710,890 (GRCm39) probably benign Het
Tyr T C 7: 87,141,855 (GRCm39) Y158C probably null Het
U2af1l4 G T 7: 30,262,773 (GRCm39) probably benign Het
Ubqlnl C T 7: 103,798,925 (GRCm39) V191M probably benign Het
Vmn2r86 T A 10: 130,282,939 (GRCm39) D559V probably damaging Het
Wfikkn2 T A 11: 94,129,902 (GRCm39) T80S probably benign Het
Zdhhc2 T A 8: 40,917,183 (GRCm39) probably null Het
Zfp521 T C 18: 13,977,111 (GRCm39) K1101E possibly damaging Het
Zfp595 A T 13: 67,465,229 (GRCm39) F345I probably benign Het
Zswim2 T A 2: 83,745,739 (GRCm39) R566S probably benign 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
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
R6852: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'- ACCTCTGCATCTGTAGGGAG -3'
(R):5'- GTTCACTCTTTGCTGCAACAGG -3'

Sequencing Primer
(F):5'- GAGAATGTGAATCCTGGATGTCTATC -3'
(R):5'- TTGCTGCAACAGGTTGTAATGAGAAC -3'
Posted On 2015-11-11