Incidental Mutation 'R0225:Lhx9'
ID 33826
Institutional Source Beutler Lab
Gene Symbol Lhx9
Ensembl Gene ENSMUSG00000019230
Gene Name LIM homeobox protein 9
Synonyms 3110009O07Rik, Lhx9 alpha, LH2B
MMRRC Submission 038470-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.787) question?
Stock # R0225 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 138752924-138776315 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 138766417 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 124 (C124S)
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: C133S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: C133S

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: C124S

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: C124S

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: C124S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: C124S

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: C133S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: C133S

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: C124S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: C124S

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 possibly damaging
Transcript: ENSMUST00000194557
AA Change: M65K

PolyPhen 2 Score 0.713 (Sensitivity: 0.86; Specificity: 0.92)
Meta Mutation Damage Score 0.9659 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency 100% (67/67)
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 T A 7: 120,139,378 (GRCm39) L1470Q probably damaging Het
Abraxas2 G A 7: 132,476,584 (GRCm39) R105Q probably damaging Het
Arhgap23 G T 11: 97,335,154 (GRCm39) V70L probably benign Het
Bicd1 T C 6: 149,414,448 (GRCm39) I387T probably benign Het
Cd59b G A 2: 103,909,286 (GRCm39) probably null Het
Chn2 T C 6: 54,267,436 (GRCm39) probably benign Het
Col18a1 T C 10: 76,924,748 (GRCm39) S14G possibly damaging Het
Col5a2 A G 1: 45,446,195 (GRCm39) I461T probably benign Het
Dele1 G A 18: 38,394,317 (GRCm39) V505I probably benign Het
Dnlz T C 2: 26,241,380 (GRCm39) N116S probably damaging Het
Esyt2 A G 12: 116,331,330 (GRCm39) N736S probably damaging Het
F11 T C 8: 45,702,114 (GRCm39) T267A probably benign Het
Fam234b T G 6: 135,194,072 (GRCm39) S242A possibly damaging Het
Gadd45b A G 10: 80,766,181 (GRCm39) N11S probably benign Het
Garnl3 T C 2: 32,896,816 (GRCm39) T608A possibly damaging Het
Gata3 T C 2: 9,879,620 (GRCm39) T119A probably benign Het
Gm10647 A G 9: 66,705,777 (GRCm39) probably benign Het
Gm10936 G A 10: 117,084,035 (GRCm39) noncoding transcript Het
Gzmd A G 14: 56,367,161 (GRCm39) W244R probably damaging Het
Hdac2 T A 10: 36,865,180 (GRCm39) D131E probably benign Het
Hira T A 16: 18,774,921 (GRCm39) F949I probably benign Het
Ighv15-2 T G 12: 114,528,657 (GRCm39) probably benign Het
Il3 A G 11: 54,156,506 (GRCm39) probably null Het
Itgae A C 11: 73,002,168 (GRCm39) M91L probably benign Het
Jkampl A G 6: 73,446,402 (GRCm39) L49P possibly damaging Het
Kat2b A G 17: 53,948,238 (GRCm39) E336G probably damaging Het
Kctd21 T A 7: 96,997,298 (GRCm39) I257N probably benign Het
Kif23 C G 9: 61,832,976 (GRCm39) probably benign Het
Lgi3 A T 14: 70,770,261 (GRCm39) I109L probably benign Het
Lipo4 A G 19: 33,479,006 (GRCm39) V278A probably benign Het
Lrch3 T A 16: 32,782,124 (GRCm39) probably benign Het
Lrp1b T C 2: 40,486,995 (GRCm39) E142G probably damaging Het
Map9 G A 3: 82,267,290 (GRCm39) probably benign Het
Miox C T 15: 89,218,657 (GRCm39) probably benign Het
Mndal A T 1: 173,685,079 (GRCm39) probably benign Het
Mug2 G T 6: 122,051,673 (GRCm39) V952L possibly damaging Het
Nepn A T 10: 52,276,533 (GRCm39) T29S probably damaging Het
Or14a260 A G 7: 85,984,803 (GRCm39) I267T probably benign Het
Or4k5 T G 14: 50,386,092 (GRCm39) K80Q probably damaging Het
Or8d1b A G 9: 38,887,574 (GRCm39) I201V probably benign Het
Or8k53 T C 2: 86,178,072 (GRCm39) I13V possibly damaging Het
Phf3 A T 1: 30,844,146 (GRCm39) D1604E probably benign Het
Plekhn1 T C 4: 156,312,700 (GRCm39) R53G probably benign Het
Prickle1 A G 15: 93,408,658 (GRCm39) L47P possibly damaging Het
Ptar1 T A 19: 23,695,459 (GRCm39) C309S probably benign Het
Rapgef2 A T 3: 79,011,412 (GRCm39) S224R probably damaging Het
Rimoc1 T C 15: 4,015,776 (GRCm39) K263E probably damaging Het
Siglecg G A 7: 43,060,595 (GRCm39) G325D probably damaging Het
Skor2 A T 18: 76,946,793 (GRCm39) I172F unknown Het
Slc9a1 A G 4: 133,147,916 (GRCm39) K645E probably benign Het
St14 T A 9: 31,019,580 (GRCm39) probably null Het
Tas2r120 T A 6: 132,634,552 (GRCm39) Y211* probably null Het
Tbxa2r C A 10: 81,168,734 (GRCm39) T141K possibly damaging Het
Tpd52l1 A G 10: 31,255,252 (GRCm39) S32P probably damaging Het
Ttn T A 2: 76,540,468 (GRCm39) R34173W probably damaging Het
Ttn C A 2: 76,623,474 (GRCm39) V15368L possibly damaging Het
Tyms A G 5: 30,268,256 (GRCm39) I148T probably damaging Het
Vmn1r45 A T 6: 89,910,492 (GRCm39) Y159* probably null Het
Vmn1r58 A C 7: 5,413,865 (GRCm39) S122A probably benign Het
Vmn2r13 C A 5: 109,322,915 (GRCm39) V125L probably benign Het
Vmn2r92 C T 17: 18,388,219 (GRCm39) A408V probably damaging Het
Vps13b T C 15: 35,887,407 (GRCm39) I3272T probably benign Het
Wfdc8 A G 2: 164,439,105 (GRCm39) Y426H probably benign Het
Zfp948 A T 17: 21,807,556 (GRCm39) K249N probably damaging Het
Zfyve1 A G 12: 83,601,847 (GRCm39) probably benign Het
Zyg11a G A 4: 108,061,838 (GRCm39) T321I 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
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
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'- CCATTGAAGTAAGGCAAAGCCAAGC -3'
(R):5'- ATTCACTAGGACCAGAGGAGGTCAC -3'

Sequencing Primer
(F):5'- CAGCTCCGTGTAGCTCAG -3'
(R):5'- TCACCGAGCAAGTAAAGCTG -3'
Posted On 2013-05-09