Incidental Mutation 'R7264:Lhx9'
ID |
564787 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lhx9
|
Ensembl Gene |
ENSMUSG00000019230 |
Gene Name |
LIM homeobox protein 9 |
Synonyms |
3110009O07Rik, Lhx9 alpha, LH2B |
MMRRC Submission |
045354-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.787)
|
Stock # |
R7264 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
1 |
Chromosomal Location |
138752924-138776315 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 138760489 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glycine
at position 296
(D296G)
|
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: D296G
PolyPhen 2
Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000019374 Gene: ENSMUSG00000019230 AA Change: D296G
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 |
possibly damaging
Transcript: ENSMUST00000046870
AA Change: D287G
PolyPhen 2
Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000036480 Gene: ENSMUSG00000019230 AA Change: D287G
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: D287G
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000091198 Gene: ENSMUSG00000019230 AA Change: D287G
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: D296G
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000107657 Gene: ENSMUSG00000019230 AA Change: D296G
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: D287G
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000107661 Gene: ENSMUSG00000019230 AA Change: D287G
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: 99.9%
- 10x: 99.6%
- 20x: 98.6%
|
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: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adora3 |
C |
A |
3: 105,812,141 (GRCm39) |
T9K |
probably benign |
Het |
Ankib1 |
T |
A |
5: 3,805,739 (GRCm39) |
N176I |
probably damaging |
Het |
Ankle2 |
G |
A |
5: 110,385,689 (GRCm39) |
G346D |
probably damaging |
Het |
Anks1b |
T |
A |
10: 90,348,732 (GRCm39) |
M800K |
probably benign |
Het |
Arhgef16 |
C |
T |
4: 154,365,387 (GRCm39) |
G576D |
probably damaging |
Het |
C2cd2 |
C |
A |
16: 97,677,419 (GRCm39) |
|
probably null |
Het |
Cacna1c |
T |
C |
6: 118,579,156 (GRCm39) |
N1847S |
|
Het |
Camta1 |
A |
G |
4: 151,537,856 (GRCm39) |
I108T |
probably damaging |
Het |
Catsper4 |
TTCTC |
TTC |
4: 133,954,423 (GRCm39) |
|
probably null |
Het |
Cep192 |
A |
G |
18: 67,953,426 (GRCm39) |
Y481C |
probably damaging |
Het |
Cep250 |
A |
G |
2: 155,821,071 (GRCm39) |
E887G |
probably damaging |
Het |
Clcn1 |
C |
A |
6: 42,275,772 (GRCm39) |
A298D |
probably damaging |
Het |
Col11a1 |
A |
G |
3: 113,979,248 (GRCm39) |
N1305S |
unknown |
Het |
Depdc5 |
T |
C |
5: 33,125,089 (GRCm39) |
V1155A |
probably benign |
Het |
Dnah1 |
A |
T |
14: 30,991,851 (GRCm39) |
D3050E |
probably benign |
Het |
Dnah7a |
T |
C |
1: 53,557,973 (GRCm39) |
D2147G |
probably benign |
Het |
Fbxl4 |
T |
C |
4: 22,386,145 (GRCm39) |
Y251H |
possibly damaging |
Het |
Gm19410 |
A |
G |
8: 36,252,920 (GRCm39) |
M622V |
probably benign |
Het |
Gm3402 |
T |
A |
5: 146,451,472 (GRCm39) |
M110K |
probably damaging |
Het |
Gm8257 |
T |
A |
14: 44,893,817 (GRCm39) |
E82D |
probably damaging |
Het |
Gne |
T |
A |
4: 44,042,175 (GRCm39) |
I498F |
probably damaging |
Het |
Grep1 |
A |
G |
17: 23,931,308 (GRCm39) |
S200P |
not run |
Het |
Gstcd |
C |
T |
3: 132,790,540 (GRCm39) |
V76I |
probably benign |
Het |
Hgs |
G |
T |
11: 120,365,139 (GRCm39) |
V176L |
probably benign |
Het |
Hrob |
T |
A |
11: 102,146,422 (GRCm39) |
C233S |
probably benign |
Het |
Igbp1b |
T |
C |
6: 138,635,108 (GRCm39) |
N112S |
possibly damaging |
Het |
Itga11 |
A |
T |
9: 62,653,190 (GRCm39) |
T355S |
probably benign |
Het |
Lama1 |
A |
T |
17: 68,050,292 (GRCm39) |
H301L |
|
Het |
Lrp1 |
C |
T |
10: 127,427,962 (GRCm39) |
G537D |
probably damaging |
Het |
Mroh2b |
A |
G |
15: 4,950,844 (GRCm39) |
I581V |
possibly damaging |
Het |
Mrps36 |
A |
G |
13: 100,875,707 (GRCm39) |
S36P |
probably benign |
Het |
Or52z13 |
T |
A |
7: 103,246,955 (GRCm39) |
I144N |
probably damaging |
Het |
Plcb4 |
A |
T |
2: 135,807,000 (GRCm39) |
N547I |
probably benign |
Het |
Plch2 |
T |
A |
4: 155,083,424 (GRCm39) |
M505L |
probably damaging |
Het |
Prg4 |
T |
A |
1: 150,329,818 (GRCm39) |
N154Y |
not run |
Het |
Rev1 |
A |
T |
1: 38,124,682 (GRCm39) |
V420D |
probably damaging |
Het |
Rin3 |
A |
G |
12: 102,356,374 (GRCm39) |
I972V |
probably benign |
Het |
Rtel1 |
T |
C |
2: 180,993,654 (GRCm39) |
L775P |
not run |
Het |
Scarf2 |
G |
T |
16: 17,621,154 (GRCm39) |
C274F |
possibly damaging |
Het |
Serinc2 |
C |
T |
4: 130,152,052 (GRCm39) |
V271I |
probably benign |
Het |
Slpi |
C |
A |
2: 164,198,322 (GRCm39) |
|
probably benign |
Het |
Spopfm1 |
C |
T |
3: 94,173,045 (GRCm39) |
H14Y |
possibly damaging |
Het |
Stxbp6 |
T |
C |
12: 44,948,782 (GRCm39) |
D109G |
probably damaging |
Het |
Tmem74 |
G |
A |
15: 43,730,864 (GRCm39) |
L60F |
probably benign |
Het |
Trhde |
C |
T |
10: 114,636,776 (GRCm39) |
G144S |
possibly damaging |
Het |
Trrap |
T |
C |
5: 144,751,333 (GRCm39) |
S1610P |
probably benign |
Het |
Ttc33 |
C |
T |
15: 5,246,718 (GRCm39) |
Q175* |
probably null |
Het |
Usp34 |
A |
G |
11: 23,283,566 (GRCm39) |
T106A |
probably benign |
Het |
Vmn1r204 |
A |
G |
13: 22,741,167 (GRCm39) |
D266G |
probably benign |
Het |
Wdfy3 |
C |
A |
5: 102,003,389 (GRCm39) |
A2905S |
probably benign |
Het |
Wfs1 |
A |
G |
5: 37,125,190 (GRCm39) |
L567P |
probably damaging |
Het |
Zfp42 |
T |
C |
8: 43,749,312 (GRCm39) |
E63G |
probably damaging |
Het |
Zfp957 |
A |
G |
14: 79,451,080 (GRCm39) |
F240L |
probably damaging |
Het |
Zgrf1 |
A |
T |
3: 127,357,218 (GRCm39) |
M815L |
probably benign |
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 |
|
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'- CTGCATCTGTAGGGAGAATGTG -3'
(R):5'- TCACTCTTTGCTGCAACAGG -3'
Sequencing Primer
(F):5'- GAGAATGTGAATCCTGGATGTCTATC -3'
(R):5'- TTGCTGCAACAGGTTGTAATGAGAAC -3'
|
Posted On |
2019-06-26 |