Incidental Mutation 'IGL02982:Lhx9'
ID 406570
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lhx9
Ensembl Gene ENSMUSG00000019230
Gene Name LIM homeobox protein 9
Synonyms 3110009O07Rik, Lhx9 alpha, LH2B
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.801) question?
Stock # IGL02982
Quality Score
Status
Chromosome 1
Chromosomal Location 138825186-138848577 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 138838611 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 155 (H155Q)
Ref Sequence ENSEMBL: ENSMUSP00000107657 (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: H155Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: H155Q

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: H146Q

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: H146Q

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: H146Q

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: H146Q

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: H155Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: H155Q

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: H146Q

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: H146Q

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
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam5 G T 8: 24,804,431 A384D probably benign Het
Adamts19 T A 18: 59,024,518 C961S probably damaging Het
Agbl2 G A 2: 90,805,815 C565Y probably damaging Het
Aox3 G A 1: 58,127,687 E190K probably benign Het
Arf2 T G 11: 103,981,776 D74E probably damaging Het
Bptf T G 11: 107,076,674 D960A probably damaging Het
Ccdc180 G T 4: 45,903,840 probably benign Het
Ces1a A G 8: 93,044,975 F65L probably damaging Het
Def8 T C 8: 123,456,539 probably benign Het
Fat4 T C 3: 38,890,843 L1295P probably damaging Het
Filip1l A G 16: 57,572,232 H1061R probably damaging Het
Fut2 C T 7: 45,650,769 G193E possibly damaging Het
Gldc A G 19: 30,145,145 probably null Het
Gm597 T C 1: 28,778,054 H299R probably damaging Het
Golgb1 A C 16: 36,925,810 D2917A probably damaging Het
Gpc5 G A 14: 115,369,988 C334Y probably damaging Het
Gpsm1 T A 2: 26,324,859 L252Q probably damaging Het
Iars C T 13: 49,709,709 R546C probably benign Het
Kbtbd8 G T 6: 95,126,566 V399L probably benign Het
Kcnd2 A T 6: 21,217,149 D284V probably damaging Het
Kcnj6 T C 16: 94,832,517 K227R possibly damaging Het
Mcm9 A G 10: 53,625,826 V221A probably damaging Het
Myo9a A T 9: 59,908,208 K2237* probably null Het
Ntf3 A T 6: 126,102,377 D55E probably damaging Het
Olfr1229 G T 2: 89,283,109 T29K probably damaging Het
Olfr61 A T 7: 140,637,952 I84F probably benign Het
Plek T A 11: 16,981,826 I342F probably damaging Het
Polrmt A G 10: 79,738,348 Y853H probably damaging Het
Psg29 A G 7: 17,211,707 T401A probably damaging Het
Ptprb A G 10: 116,322,628 T822A probably benign Het
Ptprq A C 10: 107,586,684 F1616V probably damaging Het
Rpe65 T A 3: 159,600,361 V19E probably damaging Het
Scamp2 G A 9: 57,581,549 A178T probably benign Het
Spta1 A G 1: 174,187,288 I445V probably benign Het
Tas2r135 A G 6: 42,406,253 E242G probably benign Het
Ttc22 T C 4: 106,638,586 V379A probably damaging Het
Unc5d C T 8: 28,652,853 G857E probably damaging Het
Usp28 A G 9: 49,018,439 I43V probably benign Het
Vmn2r68 A T 7: 85,234,441 M152K probably benign Het
Wrn C T 8: 33,343,066 G133R probably damaging Het
Zfyve26 G A 12: 79,263,870 T187M probably damaging Het
Zic2 A G 14: 122,478,567 E367G probably damaging Het
Other mutations in Lhx9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00955:Lhx9 APN 1 138828680 missense possibly damaging 0.74
IGL01624:Lhx9 APN 1 138832783 nonsense probably null
IGL02149:Lhx9 APN 1 138831434 missense probably damaging 1.00
IGL02452:Lhx9 APN 1 138841842 missense probably damaging 1.00
R0123:Lhx9 UTSW 1 138838679 missense probably damaging 1.00
R0134:Lhx9 UTSW 1 138838679 missense probably damaging 1.00
R0141:Lhx9 UTSW 1 138840006 missense possibly damaging 0.86
R0225:Lhx9 UTSW 1 138838679 missense probably damaging 1.00
R0281:Lhx9 UTSW 1 138832904 missense probably benign 0.00
R1460:Lhx9 UTSW 1 138838709 splice site probably benign
R1932:Lhx9 UTSW 1 138842009 start gained probably benign
R4738:Lhx9 UTSW 1 138832748 missense probably damaging 1.00
R4792:Lhx9 UTSW 1 138838351 missense possibly damaging 0.87
R4820:Lhx9 UTSW 1 138838367 missense probably benign 0.00
R4877:Lhx9 UTSW 1 138838354 missense probably benign 0.04
R6035:Lhx9 UTSW 1 138838543 missense possibly damaging 0.67
R6035:Lhx9 UTSW 1 138838543 missense possibly damaging 0.67
R6825:Lhx9 UTSW 1 138841806 frame shift probably null
R6852:Lhx9 UTSW 1 138841806 frame shift probably null
R6853:Lhx9 UTSW 1 138841806 frame shift probably null
R7264:Lhx9 UTSW 1 138832751 missense probably damaging 0.98
R8097:Lhx9 UTSW 1 138838351 missense probably damaging 0.97
R8164:Lhx9 UTSW 1 138832780 missense probably damaging 1.00
R8245:Lhx9 UTSW 1 138838441 missense probably benign 0.24
R8278:Lhx9 UTSW 1 138838586 missense probably damaging 0.98
R8951:Lhx9 UTSW 1 138841966 missense probably damaging 1.00
Z1177:Lhx9 UTSW 1 138831498 missense probably damaging 0.99
Posted On 2016-08-02