Incidental Mutation 'R2393:Lhx6'
| ID |
247846 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx6
|
| Ensembl Gene |
ENSMUSG00000026890 |
| Gene Name |
LIM homeobox protein 6 |
| Synonyms |
|
| MMRRC Submission |
040361-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.926)
|
| Stock # |
R2393 (G1)
|
| Quality Score |
160 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
35971965-35995420 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 35981402 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 63
(D63G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135776
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000112960]
[ENSMUST00000112961]
[ENSMUST00000112963]
[ENSMUST00000112966]
[ENSMUST00000112967]
[ENSMUST00000136821]
[ENSMUST00000148852]
|
| AlphaFold |
Q9R1R0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000112960
AA Change: D270G
PolyPhen 2
Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: D270G
| 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: D241G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: D241G
| 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: D241G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: D241G
| 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: D241G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: D241G
| 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: D270G
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: D270G
| 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: ENSMUST00000136821
AA Change: D63G
PolyPhen 2
Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890
AA Change: D63G
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
10 |
64 |
3.17e-17 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148852
AA Change: D241G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: D241G
| 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
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000185171
|
| Meta Mutation Damage Score |
0.2897 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.7%
|
| Validation Efficiency |
100% (54/54) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca13 |
T |
A |
11: 9,225,057 (GRCm39) |
L512* |
probably null |
Het |
| Adam4 |
A |
T |
12: 81,467,485 (GRCm39) |
F379I |
probably benign |
Het |
| Ano6 |
C |
G |
15: 95,863,906 (GRCm39) |
|
probably benign |
Het |
| Apc2 |
A |
G |
10: 80,148,903 (GRCm39) |
E1319G |
possibly damaging |
Het |
| Arfgef3 |
A |
G |
10: 18,473,535 (GRCm39) |
V1588A |
possibly damaging |
Het |
| Arl8a |
T |
A |
1: 135,080,604 (GRCm39) |
V93E |
probably damaging |
Het |
| Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
| Cd200r2 |
T |
A |
16: 44,729,630 (GRCm39) |
I95N |
probably damaging |
Het |
| Cd209d |
A |
G |
8: 3,928,436 (GRCm39) |
|
probably null |
Het |
| Cep290 |
A |
G |
10: 100,397,100 (GRCm39) |
|
probably null |
Het |
| Chd2 |
G |
T |
7: 73,157,631 (GRCm39) |
D171E |
possibly damaging |
Het |
| Chrna7 |
G |
A |
7: 62,748,994 (GRCm39) |
A496V |
probably damaging |
Het |
| Col9a2 |
C |
G |
4: 120,911,455 (GRCm39) |
R599G |
probably damaging |
Het |
| Colgalt1 |
C |
G |
8: 72,076,385 (GRCm39) |
T612S |
probably benign |
Het |
| Copg2 |
T |
C |
6: 30,787,893 (GRCm39) |
K602E |
probably benign |
Het |
| Crtc1 |
T |
A |
8: 70,840,808 (GRCm39) |
T473S |
probably benign |
Het |
| Ctbp2 |
A |
T |
7: 132,625,290 (GRCm39) |
|
probably null |
Het |
| Edem1 |
T |
G |
6: 108,829,504 (GRCm39) |
M541R |
probably damaging |
Het |
| Ehmt1 |
A |
C |
2: 24,696,229 (GRCm39) |
V953G |
probably damaging |
Het |
| Fabp3 |
C |
T |
4: 130,206,180 (GRCm39) |
T57I |
probably benign |
Het |
| Fgfr2 |
T |
C |
7: 129,828,968 (GRCm39) |
|
probably null |
Het |
| Focad |
A |
G |
4: 88,039,567 (GRCm39) |
D10G |
probably damaging |
Het |
| Gfus |
G |
T |
15: 75,798,200 (GRCm39) |
L191I |
probably damaging |
Het |
| Gm5901 |
G |
T |
7: 105,026,996 (GRCm39) |
V255F |
possibly damaging |
Het |
| Hsp90aa1 |
T |
C |
12: 110,659,840 (GRCm39) |
N416S |
probably damaging |
Het |
| Hspb1 |
T |
C |
5: 135,917,950 (GRCm39) |
F142L |
probably benign |
Het |
| Il17re |
C |
T |
6: 113,439,314 (GRCm39) |
H75Y |
possibly damaging |
Het |
| Kctd3 |
A |
G |
1: 188,713,568 (GRCm39) |
I389T |
probably damaging |
Het |
| Mepe |
A |
G |
5: 104,485,327 (GRCm39) |
T156A |
possibly damaging |
Het |
| Met |
A |
G |
6: 17,534,197 (GRCm39) |
Y680C |
probably damaging |
Het |
| Mrgpra3 |
T |
C |
7: 47,239,365 (GRCm39) |
Y187C |
possibly damaging |
Het |
| Mst1 |
T |
G |
9: 107,960,151 (GRCm39) |
|
probably null |
Het |
| Myh13 |
T |
A |
11: 67,231,184 (GRCm39) |
S394T |
possibly damaging |
Het |
| Nbeal1 |
T |
A |
1: 60,290,529 (GRCm39) |
V1042E |
probably damaging |
Het |
| Ndrg4 |
T |
A |
8: 96,432,839 (GRCm39) |
Y15* |
probably null |
Het |
| Neurl4 |
G |
A |
11: 69,797,900 (GRCm39) |
R720H |
probably damaging |
Het |
| Nfkbia |
A |
G |
12: 55,537,455 (GRCm39) |
|
probably benign |
Het |
| Nwd1 |
T |
A |
8: 73,389,055 (GRCm39) |
M202K |
probably benign |
Het |
| Or10d4 |
G |
T |
9: 39,580,569 (GRCm39) |
C72F |
possibly damaging |
Het |
| Or2av9 |
T |
A |
11: 58,381,546 (GRCm39) |
I12F |
probably benign |
Het |
| Pate2 |
T |
C |
9: 35,581,036 (GRCm39) |
|
probably benign |
Het |
| Pibf1 |
A |
G |
14: 99,480,368 (GRCm39) |
T715A |
probably benign |
Het |
| Pitpnm1 |
T |
C |
19: 4,160,935 (GRCm39) |
L858P |
probably benign |
Het |
| Pla2g3 |
A |
C |
11: 3,443,115 (GRCm39) |
S483R |
probably benign |
Het |
| Rad51ap2 |
T |
A |
12: 11,507,798 (GRCm39) |
D573E |
probably damaging |
Het |
| Rho |
T |
C |
6: 115,912,352 (GRCm39) |
|
probably benign |
Het |
| Rpl39l |
A |
T |
16: 9,992,328 (GRCm39) |
*52L |
probably null |
Het |
| Slco1a5 |
T |
A |
6: 142,194,501 (GRCm39) |
R381W |
possibly damaging |
Het |
| Spns3 |
T |
A |
11: 72,441,059 (GRCm39) |
|
probably benign |
Het |
| Srgap2 |
A |
G |
1: 131,259,872 (GRCm39) |
S493P |
probably benign |
Het |
| Tecpr2 |
T |
C |
12: 110,892,836 (GRCm39) |
S293P |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,583,211 (GRCm39) |
V20815M |
probably benign |
Het |
| Ushbp1 |
T |
C |
8: 71,847,132 (GRCm39) |
I167V |
probably benign |
Het |
| Wdr81 |
C |
T |
11: 75,340,231 (GRCm39) |
A1296T |
probably damaging |
Het |
| Zmym2 |
A |
G |
14: 57,158,180 (GRCm39) |
Y573C |
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 |
|
|
IGL01391:Lhx6
|
APN |
2 |
35,993,477 (GRCm39) |
missense |
probably benign |
0.00 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCTGCACTCTCAGTAATCAAGG -3'
(R):5'- AGAGCAATTGCAGGTACCCC -3'
Sequencing Primer
(F):5'- TCCTTAGGCCACACTGGAGAG -3'
(R):5'- AAGCCCCGAAGCGTGTG -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation