Incidental Mutation 'IGL01391:Lhx6'
ID |
79215 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
Gene Symbol |
Lhx6
|
Ensembl Gene |
ENSMUSG00000026890 |
Gene Name |
LIM homeobox protein 6 |
Synonyms |
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.926)
|
Stock # |
IGL01391
|
Quality Score |
|
Status
|
|
Chromosome |
2 |
Chromosomal Location |
35971965-35995420 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 35993477 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Cysteine to Serine
at position 74
(C74S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000108591
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000112960]
[ENSMUST00000112961]
[ENSMUST00000112963]
[ENSMUST00000112966]
[ENSMUST00000112967]
[ENSMUST00000148852]
|
AlphaFold |
Q9R1R0 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000112960
AA Change: C74S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000108584 Gene: ENSMUSG00000026890 AA Change: C74S
Domain | Start | End | E-Value | Type |
low complexity region
|
71 |
94 |
N/A |
INTRINSIC |
LIM
|
98 |
151 |
7.34e-13 |
SMART |
LIM
|
159 |
213 |
3.17e-17 |
SMART |
HOX
|
248 |
310 |
1.1e-23 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000112961
AA Change: C45S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000108585 Gene: ENSMUSG00000026890 AA Change: C45S
Domain | Start | End | E-Value | Type |
low complexity region
|
42 |
65 |
N/A |
INTRINSIC |
LIM
|
69 |
122 |
7.34e-13 |
SMART |
LIM
|
130 |
184 |
3.17e-17 |
SMART |
HOX
|
219 |
281 |
1.1e-23 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000112963
AA Change: C45S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000108587 Gene: ENSMUSG00000026890 AA Change: C45S
Domain | Start | End | E-Value | Type |
low complexity region
|
42 |
65 |
N/A |
INTRINSIC |
LIM
|
69 |
122 |
7.34e-13 |
SMART |
LIM
|
130 |
184 |
3.17e-17 |
SMART |
HOX
|
219 |
281 |
1.1e-23 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000112966
AA Change: C45S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000108590 Gene: ENSMUSG00000026890 AA Change: C45S
Domain | Start | End | E-Value | Type |
low complexity region
|
42 |
65 |
N/A |
INTRINSIC |
LIM
|
69 |
122 |
7.34e-13 |
SMART |
LIM
|
130 |
184 |
3.17e-17 |
SMART |
HOX
|
219 |
281 |
1.1e-23 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000112967
AA Change: C74S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000108591 Gene: ENSMUSG00000026890 AA Change: C74S
Domain | Start | End | E-Value | Type |
low complexity region
|
71 |
94 |
N/A |
INTRINSIC |
LIM
|
98 |
151 |
7.34e-13 |
SMART |
LIM
|
159 |
213 |
3.17e-17 |
SMART |
HOX
|
248 |
310 |
1.1e-23 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137436
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000148852
AA Change: C45S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000135693 Gene: ENSMUSG00000026890 AA Change: C45S
Domain | Start | End | E-Value | Type |
low complexity region
|
42 |
65 |
N/A |
INTRINSIC |
LIM
|
69 |
122 |
7.34e-13 |
SMART |
LIM
|
130 |
184 |
3.17e-17 |
SMART |
HOX
|
219 |
281 |
1.1e-23 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000187180
|
Coding Region Coverage |
|
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 a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017] PHENOTYPE: Homozygous mutation of this gene results in impaired migration and specification of cortical interneurons, postnatal lethality and weakness. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Ap3m2 |
T |
A |
8: 23,289,663 (GRCm39) |
I147F |
probably benign |
Het |
Areg |
T |
A |
5: 91,288,954 (GRCm39) |
S87T |
probably damaging |
Het |
Arid1b |
T |
A |
17: 5,369,133 (GRCm39) |
|
probably benign |
Het |
Arl6ip6 |
A |
G |
2: 53,082,156 (GRCm39) |
R8G |
probably benign |
Het |
Brms1 |
A |
G |
19: 5,096,723 (GRCm39) |
E135G |
possibly damaging |
Het |
Ccser1 |
A |
G |
6: 61,615,505 (GRCm39) |
|
probably benign |
Het |
Dock3 |
A |
T |
9: 106,784,433 (GRCm39) |
M258K |
possibly damaging |
Het |
Epb41l4a |
T |
G |
18: 33,934,678 (GRCm39) |
D562A |
possibly damaging |
Het |
Etaa1 |
G |
A |
11: 17,896,005 (GRCm39) |
T704I |
probably damaging |
Het |
Fer1l4 |
T |
A |
2: 155,878,376 (GRCm39) |
H972L |
probably damaging |
Het |
Foxn1 |
A |
G |
11: 78,252,320 (GRCm39) |
M356T |
probably damaging |
Het |
Gfral |
C |
A |
9: 76,072,107 (GRCm39) |
G388* |
probably null |
Het |
Gm12258 |
A |
G |
11: 58,739,520 (GRCm39) |
T3A |
probably benign |
Het |
Hoxa5 |
T |
C |
6: 52,181,311 (GRCm39) |
N7S |
probably damaging |
Het |
Itgb4 |
T |
C |
11: 115,881,746 (GRCm39) |
L765P |
probably damaging |
Het |
Jchain |
C |
T |
5: 88,669,383 (GRCm39) |
C90Y |
probably damaging |
Het |
Klhl40 |
A |
G |
9: 121,607,983 (GRCm39) |
Y381C |
probably damaging |
Het |
Magel2 |
A |
G |
7: 62,030,632 (GRCm39) |
S1179G |
unknown |
Het |
Mapre3 |
T |
C |
5: 31,022,241 (GRCm39) |
I236T |
probably damaging |
Het |
Mcf2l |
A |
T |
8: 13,064,010 (GRCm39) |
|
probably null |
Het |
Med13 |
A |
T |
11: 86,219,323 (GRCm39) |
H374Q |
probably benign |
Het |
Meioc |
A |
G |
11: 102,565,113 (GRCm39) |
Y187C |
probably benign |
Het |
Myh1 |
G |
A |
11: 67,108,689 (GRCm39) |
M1368I |
probably benign |
Het |
Or14a258 |
A |
T |
7: 86,035,208 (GRCm39) |
I220N |
possibly damaging |
Het |
Or8b54 |
A |
G |
9: 38,686,826 (GRCm39) |
I92V |
probably damaging |
Het |
Phrf1 |
T |
C |
7: 140,842,394 (GRCm39) |
Y1501H |
probably damaging |
Het |
Pigb |
T |
C |
9: 72,929,573 (GRCm39) |
T337A |
probably damaging |
Het |
Pls1 |
T |
C |
9: 95,655,751 (GRCm39) |
K334E |
probably benign |
Het |
Pramel51 |
C |
T |
12: 88,145,225 (GRCm39) |
V34I |
possibly damaging |
Het |
Rab3b |
T |
C |
4: 108,797,999 (GRCm39) |
C226R |
probably damaging |
Het |
Ryr2 |
A |
T |
13: 11,571,571 (GRCm39) |
I4889N |
possibly damaging |
Het |
Serpinb1a |
G |
A |
13: 33,029,398 (GRCm39) |
S210L |
probably benign |
Het |
Slc52a3 |
A |
G |
2: 151,849,522 (GRCm39) |
I390V |
probably benign |
Het |
Slc6a7 |
C |
A |
18: 61,136,382 (GRCm39) |
A340S |
probably damaging |
Het |
Tcaf3 |
T |
C |
6: 42,570,615 (GRCm39) |
Y379C |
probably damaging |
Het |
Tex261 |
A |
G |
6: 83,748,222 (GRCm39) |
V180A |
probably benign |
Het |
Tnnt1 |
C |
T |
7: 4,517,211 (GRCm39) |
|
probably null |
Het |
Ttn |
T |
C |
2: 76,798,847 (GRCm39) |
T476A |
possibly damaging |
Het |
Vcan |
A |
G |
13: 89,852,288 (GRCm39) |
S891P |
probably benign |
Het |
Vmn2r16 |
T |
A |
5: 109,511,627 (GRCm39) |
D611E |
possibly damaging |
Het |
Vmn2r68 |
T |
C |
7: 84,886,819 (GRCm39) |
T32A |
probably benign |
Het |
Vwde |
T |
G |
6: 13,190,526 (GRCm39) |
S522R |
probably benign |
Het |
Wdr3 |
G |
A |
3: 100,054,105 (GRCm39) |
|
probably benign |
Het |
Wfs1 |
G |
T |
5: 37,128,907 (GRCm39) |
Q288K |
probably benign |
Het |
Zfp142 |
A |
G |
1: 74,618,699 (GRCm39) |
V120A |
probably damaging |
Het |
Zfp672 |
A |
G |
11: 58,208,192 (GRCm39) |
F43S |
probably damaging |
Het |
Znhit3 |
A |
T |
11: 84,802,283 (GRCm39) |
|
probably benign |
Het |
|
Other mutations in Lhx6 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00088:Lhx6
|
APN |
2 |
35,981,728 (GRCm39) |
splice site |
probably benign |
|
IGL01413:Lhx6
|
APN |
2 |
35,993,528 (GRCm39) |
missense |
probably benign |
0.24 |
IGL03154:Lhx6
|
APN |
2 |
35,984,455 (GRCm39) |
splice site |
probably null |
|
R1546:Lhx6
|
UTSW |
2 |
35,981,049 (GRCm39) |
missense |
probably benign |
0.00 |
R1630:Lhx6
|
UTSW |
2 |
35,992,913 (GRCm39) |
missense |
probably damaging |
1.00 |
R1785:Lhx6
|
UTSW |
2 |
35,977,470 (GRCm39) |
nonsense |
probably null |
|
R1786:Lhx6
|
UTSW |
2 |
35,977,470 (GRCm39) |
nonsense |
probably null |
|
R1792:Lhx6
|
UTSW |
2 |
35,977,387 (GRCm39) |
missense |
probably damaging |
1.00 |
R2126:Lhx6
|
UTSW |
2 |
35,981,336 (GRCm39) |
missense |
possibly damaging |
0.94 |
R2145:Lhx6
|
UTSW |
2 |
35,977,478 (GRCm39) |
missense |
probably benign |
0.01 |
R2167:Lhx6
|
UTSW |
2 |
35,993,371 (GRCm39) |
missense |
probably damaging |
1.00 |
R2393:Lhx6
|
UTSW |
2 |
35,981,402 (GRCm39) |
missense |
probably benign |
0.22 |
R5102:Lhx6
|
UTSW |
2 |
35,984,222 (GRCm39) |
splice site |
probably null |
|
R5418:Lhx6
|
UTSW |
2 |
35,977,378 (GRCm39) |
critical splice donor site |
probably null |
|
R6735:Lhx6
|
UTSW |
2 |
35,981,390 (GRCm39) |
missense |
probably damaging |
0.99 |
R7462:Lhx6
|
UTSW |
2 |
35,974,083 (GRCm39) |
missense |
possibly damaging |
0.86 |
R7546:Lhx6
|
UTSW |
2 |
35,993,357 (GRCm39) |
critical splice donor site |
probably null |
|
R8870:Lhx6
|
UTSW |
2 |
35,995,232 (GRCm39) |
unclassified |
probably benign |
|
R9192:Lhx6
|
UTSW |
2 |
35,981,145 (GRCm39) |
missense |
probably benign |
0.10 |
R9667:Lhx6
|
UTSW |
2 |
35,980,979 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
Posted On |
2013-11-05 |