Incidental Mutation 'R0134:Lhx9'
| ID |
21795 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx9
|
| Ensembl Gene |
ENSMUSG00000019230 |
| Gene Name |
LIM homeobox protein 9 |
| Synonyms |
3110009O07Rik, Lhx9 alpha, LH2B |
| MMRRC Submission |
038419-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.782)
|
| Stock # |
R0134 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
(trace)
|
| 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
| 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: C124S
PolyPhen 2
Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: C124S
| 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: C124S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: C124S
| 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: C133S
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: C133S
| 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: C124S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: C124S
| 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 |
possibly damaging
Transcript: ENSMUST00000194557
AA Change: M65K
PolyPhen 2
Score 0.713 (Sensitivity: 0.86; Specificity: 0.92)
|
| Meta Mutation Damage Score |
0.9659 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.2%
- 10x: 96.4%
- 20x: 93.3%
|
| Validation Efficiency |
100% (59/59) |
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110059E24Rik |
T |
C |
19: 21,575,565 (GRCm39) |
|
probably benign |
Het |
| Abca16 |
T |
A |
7: 120,139,378 (GRCm39) |
L1470Q |
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 |
| Btbd9 |
C |
T |
17: 30,493,916 (GRCm39) |
D492N |
possibly damaging |
Het |
| Cd59b |
G |
A |
2: 103,909,286 (GRCm39) |
|
probably null |
Het |
| Ddx50 |
A |
T |
10: 62,457,156 (GRCm39) |
|
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 |
| Efcab14 |
T |
C |
4: 115,597,728 (GRCm39) |
F108L |
probably damaging |
Het |
| Esyt2 |
A |
G |
12: 116,331,330 (GRCm39) |
N736S |
probably damaging |
Het |
| Exoc4 |
A |
G |
6: 33,948,881 (GRCm39) |
D908G |
possibly damaging |
Het |
| Garnl3 |
T |
C |
2: 32,896,816 (GRCm39) |
T608A |
possibly damaging |
Het |
| Hdac2 |
T |
A |
10: 36,865,180 (GRCm39) |
D131E |
probably benign |
Het |
| Hes1 |
T |
C |
16: 29,886,068 (GRCm39) |
V224A |
probably damaging |
Het |
| Hps1 |
G |
T |
19: 42,754,619 (GRCm39) |
Q277K |
probably damaging |
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 |
| Kctd21 |
T |
A |
7: 96,997,298 (GRCm39) |
I257N |
probably benign |
Het |
| Kif16b |
A |
T |
2: 142,514,295 (GRCm39) |
S1215T |
probably benign |
Het |
| Lipo4 |
A |
G |
19: 33,479,006 (GRCm39) |
V278A |
probably benign |
Het |
| Lrp1b |
T |
C |
2: 40,486,995 (GRCm39) |
E142G |
probably damaging |
Het |
| Macf1 |
T |
C |
4: 123,326,636 (GRCm39) |
M2835V |
possibly 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 |
| Nanos3 |
C |
T |
8: 84,902,763 (GRCm39) |
R133Q |
probably damaging |
Het |
| Nepn |
A |
T |
10: 52,276,533 (GRCm39) |
T29S |
probably damaging |
Het |
| Nlgn1 |
C |
T |
3: 25,490,089 (GRCm39) |
C546Y |
probably damaging |
Het |
| Or14a260 |
A |
G |
7: 85,984,803 (GRCm39) |
I267T |
probably benign |
Het |
| Or8k53 |
T |
C |
2: 86,178,072 (GRCm39) |
I13V |
possibly damaging |
Het |
| Pdgfra |
A |
G |
5: 75,327,172 (GRCm39) |
D123G |
probably damaging |
Het |
| Plekhn1 |
T |
C |
4: 156,312,700 (GRCm39) |
R53G |
probably benign |
Het |
| Pnp2 |
T |
C |
14: 51,200,634 (GRCm39) |
F100S |
probably damaging |
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 |
| Rimoc1 |
T |
C |
15: 4,015,776 (GRCm39) |
K263E |
probably damaging |
Het |
| Rxfp1 |
A |
G |
3: 79,564,783 (GRCm39) |
S327P |
probably damaging |
Het |
| Siah2 |
A |
G |
3: 58,583,536 (GRCm39) |
V250A |
probably damaging |
Het |
| Siglecg |
G |
A |
7: 43,060,595 (GRCm39) |
G325D |
probably damaging |
Het |
| Slc10a7 |
T |
A |
8: 79,423,787 (GRCm39) |
|
probably null |
Het |
| Slc9a1 |
A |
G |
4: 133,147,916 (GRCm39) |
K645E |
probably benign |
Het |
| Smarca4 |
T |
C |
9: 21,548,620 (GRCm39) |
L302P |
probably damaging |
Het |
| Smyd1 |
G |
T |
6: 71,193,749 (GRCm39) |
T392N |
probably damaging |
Het |
| Snrnp40 |
C |
G |
4: 130,271,836 (GRCm39) |
|
probably null |
Het |
| Tenm3 |
A |
T |
8: 49,127,507 (GRCm39) |
L57Q |
probably damaging |
Het |
| Tep1 |
C |
T |
14: 51,067,150 (GRCm39) |
V2269I |
possibly damaging |
Het |
| Tpd52l1 |
A |
G |
10: 31,255,252 (GRCm39) |
S32P |
probably damaging |
Het |
| Tsfm |
A |
G |
10: 126,858,798 (GRCm39) |
|
probably benign |
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 |
| Vmn2r13 |
C |
A |
5: 109,322,915 (GRCm39) |
V125L |
probably benign |
Het |
| Vps13b |
T |
C |
15: 35,887,407 (GRCm39) |
I3272T |
probably benign |
Het |
| Zfp108 |
A |
G |
7: 23,959,892 (GRCm39) |
H161R |
probably benign |
Het |
| Zfp518b |
A |
G |
5: 38,832,002 (GRCm39) |
M1T |
probably null |
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 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCATTGAAGTAAGGCAAAGCCAAGC -3'
(R):5'- ATTCACTAGGACCAGAGGAGGTCAC -3'
Sequencing Primer
(F):5'- CAGCTCCGTGTAGCTCAG -3'
(R):5'- TCACCGAGCAAGTAAAGCTG -3'
|
| Posted On |
2013-04-12 |
Incidental Mutation