Incidental Mutation 'R8278:Lhx9'
| ID |
638051 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx9
|
| Ensembl Gene |
ENSMUSG00000019230 |
| Gene Name |
LIM homeobox protein 9 |
| Synonyms |
3110009O07Rik, Lhx9 alpha, LH2B |
| MMRRC Submission |
067701-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.787)
|
| Stock # |
R8278 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
138752924-138776315 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 138766324 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Serine
at position 164
(C164S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000107657
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000019374]
[ENSMUST00000046870]
[ENSMUST00000093486]
[ENSMUST00000112026]
[ENSMUST00000112030]
[ENSMUST00000194557]
|
| AlphaFold |
Q9WUH2 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000019374
AA Change: C164S
PolyPhen 2
Score 0.710 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000019374
Gene: ENSMUSG00000019230
AA Change: C164S
| 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 benign
Transcript: ENSMUST00000046870
AA Change: C155S
PolyPhen 2
Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000036480
Gene: ENSMUSG00000019230
AA Change: C155S
| 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 |
possibly damaging
Transcript: ENSMUST00000093486
AA Change: C155S
PolyPhen 2
Score 0.649 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000091198
Gene: ENSMUSG00000019230
AA Change: C155S
| 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: C164S
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000107657
Gene: ENSMUSG00000019230
AA Change: C164S
| 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 |
possibly damaging
Transcript: ENSMUST00000112030
AA Change: C155S
PolyPhen 2
Score 0.649 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000107661
Gene: ENSMUSG00000019230
AA Change: C155S
| 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 benign
Transcript: ENSMUST00000194557
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.5%
|
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930562C15Rik |
A |
T |
16: 4,668,040 (GRCm39) |
Q477L |
probably benign |
Het |
| Adcy10 |
A |
T |
1: 165,330,857 (GRCm39) |
D40V |
probably damaging |
Het |
| Cab39l |
T |
C |
14: 59,776,562 (GRCm39) |
Y248H |
probably damaging |
Het |
| Casr |
G |
T |
16: 36,336,011 (GRCm39) |
D99E |
probably damaging |
Het |
| Cdh16 |
T |
C |
8: 105,345,107 (GRCm39) |
E364G |
probably benign |
Het |
| Cep104 |
C |
T |
4: 154,068,122 (GRCm39) |
T189I |
possibly damaging |
Het |
| Cfap418 |
T |
A |
4: 10,882,474 (GRCm39) |
|
probably null |
Het |
| Chd7 |
T |
A |
4: 8,862,485 (GRCm39) |
|
probably null |
Het |
| Chit1 |
G |
A |
1: 134,078,332 (GRCm39) |
R380Q |
probably benign |
Het |
| Cpne2 |
A |
G |
8: 95,281,316 (GRCm39) |
K174R |
probably damaging |
Het |
| Dchs2 |
T |
A |
3: 83,178,310 (GRCm39) |
I1121N |
probably damaging |
Het |
| Fgf6 |
A |
T |
6: 126,992,781 (GRCm39) |
Y78F |
probably damaging |
Het |
| H2-T10 |
A |
T |
17: 36,429,832 (GRCm39) |
N320K |
probably benign |
Het |
| Heatr3 |
A |
T |
8: 88,883,361 (GRCm39) |
N398I |
possibly damaging |
Het |
| Hrh4 |
T |
C |
18: 13,140,284 (GRCm39) |
S60P |
probably damaging |
Het |
| Ikbip |
A |
G |
10: 90,932,190 (GRCm39) |
H278R |
probably benign |
Het |
| Jmy |
A |
T |
13: 93,601,224 (GRCm39) |
I394N |
probably damaging |
Het |
| Klhl8 |
T |
C |
5: 104,022,107 (GRCm39) |
E314G |
probably benign |
Het |
| Loxl3 |
G |
T |
6: 83,025,697 (GRCm39) |
G352C |
probably damaging |
Het |
| Lrrk1 |
A |
G |
7: 65,928,432 (GRCm39) |
F1232S |
probably benign |
Het |
| Mpnd |
A |
G |
17: 56,319,469 (GRCm39) |
T311A |
probably benign |
Het |
| Mpp7 |
A |
T |
18: 7,444,025 (GRCm39) |
D132E |
probably benign |
Het |
| Nck2 |
T |
C |
1: 43,593,740 (GRCm39) |
S316P |
probably damaging |
Het |
| Nckap5 |
T |
C |
1: 125,955,509 (GRCm39) |
S348G |
probably damaging |
Het |
| Nyap1 |
C |
T |
5: 137,730,077 (GRCm39) |
R790H |
probably damaging |
Het |
| Or5b124 |
C |
T |
19: 13,610,958 (GRCm39) |
T161I |
possibly damaging |
Het |
| Pdcd11 |
G |
A |
19: 47,094,736 (GRCm39) |
V507I |
probably damaging |
Het |
| Pdzd2 |
T |
C |
15: 12,375,995 (GRCm39) |
H1380R |
probably benign |
Het |
| Pgap1 |
C |
T |
1: 54,529,430 (GRCm39) |
V763I |
probably benign |
Het |
| Pnma8b |
G |
T |
7: 16,680,263 (GRCm39) |
V416L |
probably damaging |
Het |
| Prkn |
A |
T |
17: 12,269,609 (GRCm39) |
N421Y |
probably benign |
Het |
| Prpf4 |
T |
C |
4: 62,333,493 (GRCm39) |
|
probably null |
Het |
| Psmb5 |
C |
T |
14: 54,855,342 (GRCm39) |
G36D |
probably benign |
Het |
| Ptprq |
A |
G |
10: 107,522,239 (GRCm39) |
S571P |
possibly damaging |
Het |
| Rap1gap |
A |
C |
4: 137,444,748 (GRCm39) |
S254R |
probably damaging |
Het |
| Rufy2 |
A |
T |
10: 62,843,472 (GRCm39) |
D492V |
probably benign |
Het |
| Ryr2 |
C |
A |
13: 11,610,392 (GRCm39) |
E4145* |
probably null |
Het |
| Sgsm1 |
A |
G |
5: 113,407,958 (GRCm39) |
F898L |
probably damaging |
Het |
| Slc26a9 |
C |
A |
1: 131,689,514 (GRCm39) |
A487D |
possibly damaging |
Het |
| Slc6a15 |
T |
C |
10: 103,229,890 (GRCm39) |
|
probably null |
Het |
| Smad9 |
A |
T |
3: 54,696,687 (GRCm39) |
T251S |
probably benign |
Het |
| Socs3 |
A |
T |
11: 117,858,478 (GRCm39) |
C193* |
probably null |
Het |
| Sox6 |
T |
A |
7: 115,076,199 (GRCm39) |
D813V |
probably damaging |
Het |
| Taf2 |
A |
T |
15: 54,929,361 (GRCm39) |
L65* |
probably null |
Het |
| Taf6 |
G |
A |
5: 138,178,097 (GRCm39) |
A468V |
probably benign |
Het |
| Tmem71 |
T |
C |
15: 66,426,961 (GRCm39) |
D78G |
probably damaging |
Het |
| Tob2 |
T |
C |
15: 81,735,288 (GRCm39) |
N227S |
probably benign |
Het |
| Trim34a |
C |
A |
7: 103,898,623 (GRCm39) |
Q180K |
probably damaging |
Het |
| Ugt1a9 |
T |
C |
1: 87,999,378 (GRCm39) |
L276P |
possibly damaging |
Het |
| Wdr33 |
G |
A |
18: 31,960,405 (GRCm39) |
R23Q |
possibly damaging |
Het |
| Wnt7b |
T |
G |
15: 85,427,887 (GRCm39) |
N189H |
|
Het |
| Zfp609 |
G |
A |
9: 65,604,804 (GRCm39) |
A1308V |
possibly 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 |
|
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 |
|
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 |
|
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'- TGCCAGTGCCATTGAAGTAAG -3'
(R):5'- AAGAGGTCCTCAGCCAGAACTC -3'
Sequencing Primer
(F):5'- TGCCATTGAAGTAAGGCAAAGC -3'
(R):5'- CTGTAGACTAAGCCCTGGTACTG -3'
|
| Posted On |
2020-07-28 |
Incidental Mutation