Incidental Mutation 'R4877:Lhx9'
ID 374959
Institutional Source Beutler Lab
Gene Symbol Lhx9
Ensembl Gene ENSMUSG00000019230
Gene Name LIM homeobox protein 9
Synonyms 3110009O07Rik, Lhx9 alpha, LH2B
MMRRC Submission 042486-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.787) question?
Stock # R4877 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 138752924-138776315 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 138766092 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 232 (N232I)
Ref Sequence ENSEMBL: ENSMUSP00000036480 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000019374] [ENSMUST00000046870] [ENSMUST00000093486] [ENSMUST00000112026] [ENSMUST00000112030] [ENSMUST00000194557]
AlphaFold Q9WUH2
Predicted Effect probably benign
Transcript: ENSMUST00000019374
AA Change: N241I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: N241I

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 benign
Transcript: ENSMUST00000046870
AA Change: N232I

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: N232I

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 benign
Transcript: ENSMUST00000093486
AA Change: N232I

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: N232I

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 benign
Transcript: ENSMUST00000112026
AA Change: N241I

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: N241I

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 benign
Transcript: ENSMUST00000112030
AA Change: N232I

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: N232I

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
Meta Mutation Damage Score 0.0630 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.8%
Validation Efficiency 100% (76/76)
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc3 A G 11: 94,258,421 (GRCm39) Y475H probably damaging Het
Adamts12 G T 15: 11,327,787 (GRCm39) G1388V probably damaging Het
Anks6 C T 4: 47,030,795 (GRCm39) G601S probably damaging Het
Arhgap26 T C 18: 39,429,982 (GRCm39) probably null Het
Atp7b T A 8: 22,518,617 (GRCm39) I74F probably damaging Het
Bod1l A G 5: 41,977,337 (GRCm39) Y1326H probably benign Het
Card11 T C 5: 140,871,632 (GRCm39) S690G probably damaging Het
Cbx3 A G 6: 51,459,540 (GRCm39) E169G possibly damaging Het
Cd28 A T 1: 60,808,861 (GRCm39) M192L possibly damaging Het
Chd6 T C 2: 160,871,219 (GRCm39) probably benign Het
Cyp2c69 C T 19: 39,866,056 (GRCm39) C179Y probably damaging Het
Cyp7b1 A T 3: 18,151,457 (GRCm39) V252E probably damaging Het
Dcp2 G T 18: 44,550,659 (GRCm39) G378C probably benign Het
Dip2b A T 15: 100,058,410 (GRCm39) I196L possibly damaging Het
Erbin G A 13: 103,987,346 (GRCm39) P405S probably damaging Het
Etv1 A G 12: 38,881,292 (GRCm39) probably null Het
F830104G03Rik T G 3: 56,797,917 (GRCm39) K33T unknown Het
Fbln2 C A 6: 91,210,477 (GRCm39) H140Q probably damaging Het
Fxr1 A G 3: 34,101,847 (GRCm39) T109A probably damaging Het
Gm10110 T C 14: 90,134,785 (GRCm39) noncoding transcript Het
Gm9949 C T 18: 62,317,140 (GRCm39) probably benign Het
Grin2d A G 7: 45,504,039 (GRCm39) L604P probably damaging Het
Gstcd A T 3: 132,711,314 (GRCm39) probably benign Het
Ifna16 A G 4: 88,594,681 (GRCm39) V138A probably benign Het
Itpr2 T A 6: 146,226,703 (GRCm39) N1314I probably damaging Het
Kitl T C 10: 99,916,728 (GRCm39) V177A probably damaging Het
L3mbtl1 A T 2: 162,790,488 (GRCm39) Q185L probably damaging Het
Lnx1 T C 5: 74,788,784 (GRCm39) R111G probably benign Het
Lrrc41 A G 4: 115,936,602 (GRCm39) I72M probably damaging Het
Lrriq1 T A 10: 103,069,899 (GRCm39) D39V possibly damaging Het
Lyrm7 A G 11: 54,731,936 (GRCm39) probably benign Het
Lyst T A 13: 13,857,734 (GRCm39) Y2508N probably damaging Het
Masp2 A T 4: 148,687,328 (GRCm39) Y70F probably benign Het
Mc4r T C 18: 66,992,409 (GRCm39) I235V probably benign Het
Med12l G A 3: 59,152,214 (GRCm39) V1000M probably damaging Het
Morc2b T C 17: 33,357,712 (GRCm39) H20R probably benign Het
Ms4a1 A T 19: 11,231,857 (GRCm39) S173T probably damaging Het
Myh13 A C 11: 67,228,477 (GRCm39) D339A probably damaging Het
Nars1 A T 18: 64,633,643 (GRCm39) Y542* probably null Het
Nectin2 G A 7: 19,451,645 (GRCm39) T463I possibly damaging Het
Nrg4 A G 9: 55,166,679 (GRCm39) F64L probably benign Het
Nrxn1 T A 17: 91,395,605 (GRCm39) I184F probably benign Het
Nxph2 C T 2: 23,289,846 (GRCm39) P66L probably benign Het
Or10ag2 C T 2: 87,248,907 (GRCm39) Q170* probably null Het
Or2v1 C A 11: 49,025,608 (GRCm39) F196L probably damaging Het
Pard3 A T 8: 128,115,018 (GRCm39) T579S probably damaging Het
Patj A G 4: 98,457,295 (GRCm39) I48V possibly damaging Het
Paxbp1 T C 16: 90,841,199 (GRCm39) probably benign Het
Pou2f3 A T 9: 43,050,618 (GRCm39) N235K possibly damaging Het
Ppp2r2c A G 5: 37,026,214 (GRCm39) D17G probably damaging Het
Rgs8 A G 1: 153,568,633 (GRCm39) probably benign Het
Rnd3 A G 2: 51,038,762 (GRCm39) V42A probably damaging Het
Rp1l1 A G 14: 64,263,620 (GRCm39) R247G probably benign Het
Sec31b A T 19: 44,524,172 (GRCm39) V156D probably damaging Het
Slc22a2 T A 17: 12,833,702 (GRCm39) Y461N possibly damaging Het
Spag6l T C 16: 16,599,622 (GRCm39) K280R possibly damaging Het
Spata31d1a A G 13: 59,850,337 (GRCm39) L597P probably damaging Het
Srr G T 11: 74,798,606 (GRCm39) probably benign Het
Sry C G Y: 2,662,864 (GRCm39) Q265H unknown Het
Tgif1 A C 17: 71,156,700 (GRCm39) probably null Het
Tle3 A T 9: 61,280,781 (GRCm39) probably benign Het
Tubgcp4 A G 2: 121,020,343 (GRCm39) T439A probably benign Het
Twist1 C T 12: 34,008,350 (GRCm39) T125M probably damaging Het
Unc13a T A 8: 72,111,260 (GRCm39) D317V possibly damaging Het
Vmn1r227 T A 17: 20,955,407 (GRCm39) noncoding transcript Het
Vps72 G T 3: 95,025,498 (GRCm39) probably benign Het
Zfp184 T C 13: 22,144,498 (GRCm39) S735P possibly damaging Het
Zfp42 A T 8: 43,748,725 (GRCm39) C259S possibly damaging Het
Zmiz2 A G 11: 6,353,251 (GRCm39) H678R 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
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'- ATGGGCAACAAGGATTTGGC -3'
(R):5'- ACACTTCGAGACCCTCTTGC -3'

Sequencing Primer
(F):5'- GCAACAAGGATTTGGCTTTGC -3'
(R):5'- TCTTGCAAGGGGAATATCCAC -3'
Posted On 2016-03-17