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 |
|
| Essential gene? |
Probably essential
(E-score: 0.782)
|
| Stock # |
IGL02982
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
1 |
| Chromosomal Location |
138752924-138776315 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 138766349 bp (GRCm39)
|
| 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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam5 |
G |
T |
8: 25,294,447 (GRCm39) |
A384D |
probably benign |
Het |
| Adamts19 |
T |
A |
18: 59,157,590 (GRCm39) |
C961S |
probably damaging |
Het |
| Agbl2 |
G |
A |
2: 90,636,159 (GRCm39) |
C565Y |
probably damaging |
Het |
| Aox3 |
G |
A |
1: 58,166,846 (GRCm39) |
E190K |
probably benign |
Het |
| Arf2 |
T |
G |
11: 103,872,602 (GRCm39) |
D74E |
probably damaging |
Het |
| Bptf |
T |
G |
11: 106,967,500 (GRCm39) |
D960A |
probably damaging |
Het |
| Ccdc180 |
G |
T |
4: 45,903,840 (GRCm39) |
|
probably benign |
Het |
| Ces1a |
A |
G |
8: 93,771,603 (GRCm39) |
F65L |
probably damaging |
Het |
| Def8 |
T |
C |
8: 124,183,278 (GRCm39) |
|
probably benign |
Het |
| Fat4 |
T |
C |
3: 38,944,992 (GRCm39) |
L1295P |
probably damaging |
Het |
| Filip1l |
A |
G |
16: 57,392,595 (GRCm39) |
H1061R |
probably damaging |
Het |
| Fut2 |
C |
T |
7: 45,300,193 (GRCm39) |
G193E |
possibly damaging |
Het |
| Gldc |
A |
G |
19: 30,122,545 (GRCm39) |
|
probably null |
Het |
| Golgb1 |
A |
C |
16: 36,746,172 (GRCm39) |
D2917A |
probably damaging |
Het |
| Gpc5 |
G |
A |
14: 115,607,400 (GRCm39) |
C334Y |
probably damaging |
Het |
| Gpsm1 |
T |
A |
2: 26,214,871 (GRCm39) |
L252Q |
probably damaging |
Het |
| Iars1 |
C |
T |
13: 49,863,185 (GRCm39) |
R546C |
probably benign |
Het |
| Kbtbd8 |
G |
T |
6: 95,103,547 (GRCm39) |
V399L |
probably benign |
Het |
| Kcnd2 |
A |
T |
6: 21,217,148 (GRCm39) |
D284V |
probably damaging |
Het |
| Kcnj6 |
T |
C |
16: 94,633,376 (GRCm39) |
K227R |
possibly damaging |
Het |
| Mcm9 |
A |
G |
10: 53,501,922 (GRCm39) |
V221A |
probably damaging |
Het |
| Myo9a |
A |
T |
9: 59,815,491 (GRCm39) |
K2237* |
probably null |
Het |
| Ntf3 |
A |
T |
6: 126,079,340 (GRCm39) |
D55E |
probably damaging |
Het |
| Or13a28 |
A |
T |
7: 140,217,865 (GRCm39) |
I84F |
probably benign |
Het |
| Or4c15b |
G |
T |
2: 89,113,453 (GRCm39) |
T29K |
probably damaging |
Het |
| Plek |
T |
A |
11: 16,931,826 (GRCm39) |
I342F |
probably damaging |
Het |
| Polrmt |
A |
G |
10: 79,574,182 (GRCm39) |
Y853H |
probably damaging |
Het |
| Psg29 |
A |
G |
7: 16,945,632 (GRCm39) |
T401A |
probably damaging |
Het |
| Ptprb |
A |
G |
10: 116,158,533 (GRCm39) |
T822A |
probably benign |
Het |
| Ptprq |
A |
C |
10: 107,422,545 (GRCm39) |
F1616V |
probably damaging |
Het |
| Rpe65 |
T |
A |
3: 159,305,998 (GRCm39) |
V19E |
probably damaging |
Het |
| Scamp2 |
G |
A |
9: 57,488,832 (GRCm39) |
A178T |
probably benign |
Het |
| Spata31e5 |
T |
C |
1: 28,817,135 (GRCm39) |
H299R |
probably damaging |
Het |
| Spta1 |
A |
G |
1: 174,014,854 (GRCm39) |
I445V |
probably benign |
Het |
| Tas2r135 |
A |
G |
6: 42,383,187 (GRCm39) |
E242G |
probably benign |
Het |
| Ttc22 |
T |
C |
4: 106,495,783 (GRCm39) |
V379A |
probably damaging |
Het |
| Unc5d |
C |
T |
8: 29,142,881 (GRCm39) |
G857E |
probably damaging |
Het |
| Usp28 |
A |
G |
9: 48,929,739 (GRCm39) |
I43V |
probably benign |
Het |
| Vmn2r68 |
A |
T |
7: 84,883,649 (GRCm39) |
M152K |
probably benign |
Het |
| Wrn |
C |
T |
8: 33,833,094 (GRCm39) |
G133R |
probably damaging |
Het |
| Zfyve26 |
G |
A |
12: 79,310,644 (GRCm39) |
T187M |
probably damaging |
Het |
| Zic2 |
A |
G |
14: 122,715,979 (GRCm39) |
E367G |
probably damaging |
Het |
|
| Other mutations in Lhx9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
|
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 |
|
| Posted On |
2016-08-02 |
Incidental Mutation