Incidental Mutation 'R1346:Lhx1'
| ID |
156512 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx1
|
| Ensembl Gene |
ENSMUSG00000018698 |
| Gene Name |
LIM homeobox protein 1 |
| Synonyms |
Lim1 |
| MMRRC Submission |
039411-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1346 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
84409110-84416361 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 84412905 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 36
(E36G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000138899
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000018842]
[ENSMUST00000092827]
[ENSMUST00000184646]
|
| AlphaFold |
P63006 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000018842
AA Change: E127G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000018842
Gene: ENSMUSG00000018698
AA Change: E127G
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
3 |
54 |
5.51e-17 |
SMART |
|
LIM
|
62 |
117 |
4.24e-18 |
SMART |
|
low complexity region
|
137 |
156 |
N/A |
INTRINSIC |
|
HOX
|
180 |
242 |
1.33e-22 |
SMART |
|
low complexity region
|
315 |
327 |
N/A |
INTRINSIC |
|
low complexity region
|
349 |
367 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000092827
AA Change: E83G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000090503
Gene: ENSMUSG00000018698
AA Change: E83G
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
18 |
73 |
4.24e-18 |
SMART |
|
low complexity region
|
93 |
112 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126072
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128121
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134800
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176503
|
| SMART Domains |
Protein: ENSMUSP00000135334
Gene: ENSMUSG00000018698
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Homeobox
|
1 |
17 |
5.3e-6 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000184646
AA Change: E36G
PolyPhen 2
Score 0.545 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000138899
Gene: ENSMUSG00000018698
AA Change: E36G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
46 |
65 |
N/A |
INTRINSIC |
|
HOX
|
89 |
151 |
6.8e-25 |
SMART |
|
low complexity region
|
224 |
236 |
N/A |
INTRINSIC |
|
low complexity region
|
258 |
276 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0620 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 95.2%
- 20x: 90.1%
|
| Validation Efficiency |
98% (43/44) |
| 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 protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]
PHENOTYPE: Homozygotes for targeted null mutations are small, fail to develop head structures anterior to rhombomere 3 in the hindbrain, lack kidneys and gonads, and show aberrant trajectories of limb motor axons. Most mutants die around embryonic day 10. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3425401B19Rik |
C |
A |
14: 32,382,771 (GRCm39) |
A1065S |
probably benign |
Het |
| Ak5 |
G |
T |
3: 152,239,071 (GRCm39) |
D301E |
probably damaging |
Het |
| Akap13 |
G |
A |
7: 75,259,340 (GRCm39) |
G655S |
possibly damaging |
Het |
| Arap3 |
A |
T |
18: 38,108,971 (GRCm39) |
C1228S |
probably damaging |
Het |
| Arfgef1 |
T |
C |
1: 10,229,958 (GRCm39) |
T1248A |
probably benign |
Het |
| Atf7ip2 |
G |
A |
16: 10,052,195 (GRCm39) |
V225I |
probably damaging |
Het |
| Bdp1 |
G |
A |
13: 100,215,263 (GRCm39) |
Q374* |
probably null |
Het |
| Cacng6 |
G |
T |
7: 3,483,438 (GRCm39) |
W255C |
possibly damaging |
Het |
| Camta2 |
T |
C |
11: 70,567,293 (GRCm39) |
K628R |
possibly damaging |
Het |
| Catsperg1 |
A |
T |
7: 28,881,759 (GRCm39) |
|
probably null |
Het |
| Cers4 |
A |
G |
8: 4,565,632 (GRCm39) |
E26G |
probably damaging |
Het |
| Chfr |
A |
G |
5: 110,288,313 (GRCm39) |
D76G |
probably damaging |
Het |
| Chrng |
C |
A |
1: 87,135,985 (GRCm39) |
Q245K |
probably benign |
Het |
| Cnn2 |
T |
C |
10: 79,829,414 (GRCm39) |
|
probably benign |
Het |
| Dyrk2 |
T |
C |
10: 118,695,624 (GRCm39) |
K545E |
possibly damaging |
Het |
| Eif3d |
A |
G |
15: 77,852,754 (GRCm39) |
I9T |
probably damaging |
Het |
| Elovl7 |
A |
G |
13: 108,410,883 (GRCm39) |
I153V |
probably benign |
Het |
| Etl4 |
T |
C |
2: 20,810,955 (GRCm39) |
S1013P |
possibly damaging |
Het |
| Furin |
C |
T |
7: 80,041,932 (GRCm39) |
|
probably benign |
Het |
| Gart |
G |
T |
16: 91,425,070 (GRCm39) |
|
probably null |
Het |
| Gm572 |
G |
A |
4: 148,739,354 (GRCm39) |
V61M |
possibly damaging |
Het |
| Hspbap1 |
G |
A |
16: 35,622,035 (GRCm39) |
A127T |
probably damaging |
Het |
| Kcnh2 |
T |
C |
5: 24,527,658 (GRCm39) |
D898G |
possibly damaging |
Het |
| Kcnrg |
A |
G |
14: 61,849,144 (GRCm39) |
T202A |
probably benign |
Het |
| Lrp1 |
T |
C |
10: 127,441,735 (GRCm39) |
N167S |
probably damaging |
Het |
| Parp9 |
A |
T |
16: 35,777,267 (GRCm39) |
M171L |
probably benign |
Het |
| Pla2g4e |
G |
A |
2: 120,013,253 (GRCm39) |
R356W |
probably damaging |
Het |
| Ppp4c |
C |
T |
7: 126,391,222 (GRCm39) |
|
probably benign |
Het |
| Rab3c |
G |
A |
13: 110,397,120 (GRCm39) |
R49C |
probably damaging |
Het |
| Rbm25 |
T |
C |
12: 83,691,167 (GRCm39) |
|
probably benign |
Het |
| Sema4g |
T |
A |
19: 44,986,091 (GRCm39) |
S311T |
possibly damaging |
Het |
| Skida1 |
T |
C |
2: 18,053,090 (GRCm39) |
I21V |
possibly damaging |
Het |
| Slc25a32 |
T |
A |
15: 38,963,411 (GRCm39) |
I137F |
probably benign |
Het |
| Stard9 |
T |
C |
2: 120,543,929 (GRCm39) |
V4409A |
probably damaging |
Het |
| Stx2 |
G |
A |
5: 129,065,852 (GRCm39) |
|
probably benign |
Het |
| Timeless |
C |
T |
10: 128,078,234 (GRCm39) |
T248M |
possibly damaging |
Het |
| Tlr2 |
T |
A |
3: 83,743,900 (GRCm39) |
N728Y |
probably damaging |
Het |
| Zfp592 |
A |
T |
7: 80,687,812 (GRCm39) |
N913Y |
possibly damaging |
Het |
|
| Other mutations in Lhx1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00757:Lhx1
|
APN |
11 |
84,410,478 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1565:Lhx1
|
UTSW |
11 |
84,410,647 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1806:Lhx1
|
UTSW |
11 |
84,414,967 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2148:Lhx1
|
UTSW |
11 |
84,410,647 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2449:Lhx1
|
UTSW |
11 |
84,412,564 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3721:Lhx1
|
UTSW |
11 |
84,412,654 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3793:Lhx1
|
UTSW |
11 |
84,412,726 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4940:Lhx1
|
UTSW |
11 |
84,410,735 (GRCm39) |
nonsense |
probably null |
|
|
R5178:Lhx1
|
UTSW |
11 |
84,411,214 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R5877:Lhx1
|
UTSW |
11 |
84,413,065 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6366:Lhx1
|
UTSW |
11 |
84,413,034 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6551:Lhx1
|
UTSW |
11 |
84,412,739 (GRCm39) |
missense |
probably benign |
0.23 |
|
R7060:Lhx1
|
UTSW |
11 |
84,411,108 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7106:Lhx1
|
UTSW |
11 |
84,412,903 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7133:Lhx1
|
UTSW |
11 |
84,410,746 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7161:Lhx1
|
UTSW |
11 |
84,410,698 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7290:Lhx1
|
UTSW |
11 |
84,412,703 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8843:Lhx1
|
UTSW |
11 |
84,410,455 (GRCm39) |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGCACTTTCAGAGTCCTTGGC -3'
(R):5'- ACCCACCTTACGCAGATGTTTCG -3'
Sequencing Primer
(F):5'- AGAGTCCTTGGCATCATCCTG -3'
(R):5'- CAAATGCGCCGGTTGTG -3'
|
| Posted On |
2014-02-11 |
Incidental Mutation