Incidental Mutation 'R0574:Lhx3'
| ID |
46564 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx3
|
| Ensembl Gene |
ENSMUSG00000026934 |
| Gene Name |
LIM homeobox protein 3 |
| Synonyms |
Lim3, mLim-3, P-LIM |
| MMRRC Submission |
038764-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0574 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
26090224-26098261 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 26091323 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Glycine
at position 329
(S329G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000056822
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028302]
[ENSMUST00000054099]
|
| AlphaFold |
P50481 |
| PDB Structure |
NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex [SOLUTION NMR]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028302
AA Change: S331G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000028302
Gene: ENSMUSG00000026934
AA Change: S331G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
31 |
N/A |
INTRINSIC |
|
LIM
|
35 |
86 |
4.18e-17 |
SMART |
|
LIM
|
94 |
149 |
7.8e-17 |
SMART |
|
HOX
|
162 |
224 |
7.13e-23 |
SMART |
|
low complexity region
|
237 |
249 |
N/A |
INTRINSIC |
|
low complexity region
|
323 |
342 |
N/A |
INTRINSIC |
|
low complexity region
|
353 |
362 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000054099
AA Change: S329G
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000056822
Gene: ENSMUSG00000026934
AA Change: S329G
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
33 |
84 |
4.18e-17 |
SMART |
|
LIM
|
92 |
147 |
7.8e-17 |
SMART |
|
HOX
|
160 |
222 |
7.13e-23 |
SMART |
|
low complexity region
|
235 |
247 |
N/A |
INTRINSIC |
|
low complexity region
|
321 |
340 |
N/A |
INTRINSIC |
|
low complexity region
|
351 |
360 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127035
|
| SMART Domains |
Protein: ENSMUSP00000134884
Gene: ENSMUSG00000026934
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Homeobox
|
1 |
17 |
6.2e-5 |
PFAM |
|
low complexity region
|
35 |
47 |
N/A |
INTRINSIC |
|
low complexity region
|
121 |
140 |
N/A |
INTRINSIC |
|
low complexity region
|
151 |
160 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149637
|
| SMART Domains |
Protein: ENSMUSP00000135765
Gene: ENSMUSG00000026934
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
16 |
N/A |
INTRINSIC |
|
low complexity region
|
22 |
38 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0604 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.2%
- 20x: 92.4%
|
| Validation Efficiency |
100% (34/34) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit failure of growth and differentiation of Rathke's pouch, lack both anterior and intermediate lobes of the pituitary gland, and die perinatally, within 24 hours of birth. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700099C18Rik |
T |
C |
17: 95,068,919 (GRCm39) |
|
noncoding transcript |
Het |
| Abca14 |
A |
G |
7: 119,823,720 (GRCm39) |
I416V |
probably damaging |
Het |
| Actrt3 |
T |
C |
3: 30,653,829 (GRCm39) |
E57G |
probably benign |
Het |
| Adamts5 |
A |
G |
16: 85,696,372 (GRCm39) |
S262P |
probably damaging |
Het |
| Aldh1a2 |
T |
C |
9: 71,188,990 (GRCm39) |
|
probably null |
Het |
| Arhgap29 |
A |
G |
3: 121,801,274 (GRCm39) |
I670V |
probably benign |
Het |
| Bptf |
T |
C |
11: 106,967,353 (GRCm39) |
D1009G |
probably damaging |
Het |
| Ddr2 |
G |
T |
1: 169,809,532 (GRCm39) |
|
probably benign |
Het |
| Ift140 |
T |
A |
17: 25,270,734 (GRCm39) |
|
probably null |
Het |
| Itga1 |
A |
C |
13: 115,103,097 (GRCm39) |
S1111R |
probably damaging |
Het |
| Klk1b27 |
T |
A |
7: 43,705,525 (GRCm39) |
L199Q |
probably damaging |
Het |
| Man2b1 |
T |
G |
8: 85,823,405 (GRCm39) |
M913R |
probably benign |
Het |
| Mmp15 |
G |
A |
8: 96,092,029 (GRCm39) |
A80T |
possibly damaging |
Het |
| Mpo |
A |
T |
11: 87,686,902 (GRCm39) |
Y177F |
probably damaging |
Het |
| Mynn |
T |
C |
3: 30,670,888 (GRCm39) |
S587P |
probably benign |
Het |
| Nfkbib |
C |
T |
7: 28,461,213 (GRCm39) |
V145I |
probably benign |
Het |
| Or1o3 |
G |
T |
17: 37,573,772 (GRCm39) |
S261Y |
probably damaging |
Het |
| Or4k15 |
A |
T |
14: 50,364,139 (GRCm39) |
Y35F |
probably damaging |
Het |
| Or6k8-ps1 |
T |
C |
1: 173,979,132 (GRCm39) |
F17L |
probably benign |
Het |
| Pole2 |
G |
A |
12: 69,258,231 (GRCm39) |
|
probably benign |
Het |
| Ppargc1b |
C |
T |
18: 61,435,810 (GRCm39) |
G906D |
probably benign |
Het |
| Prl8a2 |
T |
A |
13: 27,532,883 (GRCm39) |
C32S |
probably damaging |
Het |
| Rhno1 |
A |
T |
6: 128,335,113 (GRCm39) |
|
probably null |
Het |
| Rprd2 |
T |
C |
3: 95,681,669 (GRCm39) |
E408G |
possibly damaging |
Het |
| Ryr2 |
T |
A |
13: 11,746,555 (GRCm39) |
H1999L |
probably benign |
Het |
| Shprh |
T |
C |
10: 11,038,821 (GRCm39) |
|
probably benign |
Het |
| Snx3 |
T |
A |
10: 42,378,383 (GRCm39) |
N19K |
probably benign |
Het |
| Stx8 |
C |
T |
11: 67,864,078 (GRCm39) |
T46M |
probably damaging |
Het |
| Tbc1d17 |
A |
G |
7: 44,492,547 (GRCm39) |
|
probably benign |
Het |
| Ush1c |
A |
G |
7: 45,846,228 (GRCm39) |
S855P |
possibly damaging |
Het |
| Usp54 |
A |
G |
14: 20,606,322 (GRCm39) |
V1338A |
probably benign |
Het |
| Vmn1r214 |
A |
G |
13: 23,218,663 (GRCm39) |
I52M |
probably benign |
Het |
|
| Other mutations in Lhx3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02309:Lhx3
|
APN |
2 |
26,091,385 (GRCm39) |
missense |
probably benign |
|
|
IGL02691:Lhx3
|
APN |
2 |
26,093,097 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0267:Lhx3
|
UTSW |
2 |
26,093,040 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0571:Lhx3
|
UTSW |
2 |
26,091,136 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1866:Lhx3
|
UTSW |
2 |
26,093,986 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1926:Lhx3
|
UTSW |
2 |
26,092,200 (GRCm39) |
nonsense |
probably null |
|
|
R1940:Lhx3
|
UTSW |
2 |
26,093,974 (GRCm39) |
missense |
probably benign |
0.05 |
|
R3147:Lhx3
|
UTSW |
2 |
26,091,277 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4389:Lhx3
|
UTSW |
2 |
26,091,102 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R4534:Lhx3
|
UTSW |
2 |
26,094,026 (GRCm39) |
missense |
probably benign |
|
|
R4551:Lhx3
|
UTSW |
2 |
26,091,202 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4761:Lhx3
|
UTSW |
2 |
26,091,435 (GRCm39) |
frame shift |
probably null |
|
|
R5102:Lhx3
|
UTSW |
2 |
26,091,435 (GRCm39) |
frame shift |
probably null |
|
|
R5105:Lhx3
|
UTSW |
2 |
26,091,435 (GRCm39) |
frame shift |
probably null |
|
|
R5431:Lhx3
|
UTSW |
2 |
26,091,130 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5673:Lhx3
|
UTSW |
2 |
26,093,006 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5751:Lhx3
|
UTSW |
2 |
26,091,173 (GRCm39) |
missense |
probably benign |
|
|
R6180:Lhx3
|
UTSW |
2 |
26,091,503 (GRCm39) |
missense |
probably benign |
|
|
R6262:Lhx3
|
UTSW |
2 |
26,092,435 (GRCm39) |
small deletion |
probably benign |
|
|
R7238:Lhx3
|
UTSW |
2 |
26,093,009 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8934:Lhx3
|
UTSW |
2 |
26,092,258 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Z1176:Lhx3
|
UTSW |
2 |
26,093,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TACTTCATCCAGCCAGGAAGCAGG -3'
(R):5'- TGAGAGTGCTGAAGAGACTGTCCC -3'
Sequencing Primer
(F):5'- AGAACTGCTCTCTGTGGACA -3'
(R):5'- tgtttttgttttATTGCAGATGAGCC -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation