Incidental Mutation 'R5102:Lhx6'
| ID |
392398 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx6
|
| Ensembl Gene |
ENSMUSG00000026890 |
| Gene Name |
LIM homeobox protein 6 |
| Synonyms |
|
| MMRRC Submission |
042690-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.926)
|
| Stock # |
R5102 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
35971965-35995420 bp(-) (GRCm39) |
| Type of Mutation |
splice site (3 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 35984222 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135693
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000112960]
[ENSMUST00000112960]
[ENSMUST00000112961]
[ENSMUST00000112961]
[ENSMUST00000112963]
[ENSMUST00000112963]
[ENSMUST00000112966]
[ENSMUST00000112966]
[ENSMUST00000112967]
[ENSMUST00000112967]
[ENSMUST00000136821]
[ENSMUST00000148852]
[ENSMUST00000148852]
|
| AlphaFold |
Q9R1R0 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000112960
|
| SMART Domains |
Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112960
|
| SMART Domains |
Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112961
|
| SMART Domains |
Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112961
|
| SMART Domains |
Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112963
|
| SMART Domains |
Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112963
|
| SMART Domains |
Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112966
|
| SMART Domains |
Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112966
|
| SMART Domains |
Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112967
|
| SMART Domains |
Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000112967
|
| SMART Domains |
Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000136821
|
| SMART Domains |
Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
10 |
64 |
3.17e-17 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000148852
|
| SMART Domains |
Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
| 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 null
Transcript: ENSMUST00000148852
|
| SMART Domains |
Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
| 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 |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 96.0%
- 20x: 91.3%
|
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aox4 |
C |
T |
1: 58,279,937 (GRCm39) |
R518C |
probably damaging |
Het |
| Apbb2 |
A |
T |
5: 66,469,592 (GRCm39) |
|
probably null |
Het |
| Arhgap45 |
C |
T |
10: 79,857,262 (GRCm39) |
P254S |
probably benign |
Het |
| Arl4c |
T |
C |
1: 88,629,322 (GRCm39) |
D22G |
probably damaging |
Het |
| Asxl1 |
A |
G |
2: 153,242,875 (GRCm39) |
T1142A |
probably benign |
Het |
| BC035044 |
T |
C |
6: 128,861,949 (GRCm39) |
|
probably benign |
Het |
| Bmp4 |
T |
C |
14: 46,621,458 (GRCm39) |
N362S |
probably damaging |
Het |
| Cbll1 |
G |
T |
12: 31,537,912 (GRCm39) |
T280N |
probably damaging |
Het |
| Cdh10 |
A |
T |
15: 18,986,971 (GRCm39) |
T401S |
probably benign |
Het |
| Cmklr2 |
A |
G |
1: 63,222,326 (GRCm39) |
V303A |
probably damaging |
Het |
| Cps1 |
A |
T |
1: 67,245,952 (GRCm39) |
M1148L |
probably benign |
Het |
| Crybg1 |
T |
C |
10: 43,873,832 (GRCm39) |
D1092G |
probably damaging |
Het |
| Cyth2 |
A |
G |
7: 45,460,126 (GRCm39) |
S173P |
probably damaging |
Het |
| D6Ertd527e |
A |
T |
6: 87,088,793 (GRCm39) |
I319F |
unknown |
Het |
| Dchs1 |
A |
T |
7: 105,421,384 (GRCm39) |
H345Q |
probably benign |
Het |
| Ddx50 |
A |
T |
10: 62,476,640 (GRCm39) |
V211E |
probably damaging |
Het |
| Dlx6 |
AGG |
AG |
6: 6,865,180 (GRCm39) |
|
probably null |
Het |
| Dnajb5 |
G |
A |
4: 42,956,639 (GRCm39) |
D109N |
possibly damaging |
Het |
| Dner |
A |
T |
1: 84,383,691 (GRCm39) |
N564K |
probably damaging |
Het |
| Fam234b |
T |
C |
6: 135,186,282 (GRCm39) |
S97P |
probably benign |
Het |
| Fam53b |
G |
A |
7: 132,317,684 (GRCm39) |
R60* |
probably null |
Het |
| Fmo3 |
T |
G |
1: 162,791,546 (GRCm39) |
K244Q |
probably benign |
Het |
| Golim4 |
A |
G |
3: 75,810,579 (GRCm39) |
I192T |
possibly damaging |
Het |
| Gprin1 |
T |
C |
13: 54,887,576 (GRCm39) |
M233V |
probably benign |
Het |
| Gtf2f1 |
A |
T |
17: 57,310,626 (GRCm39) |
V443D |
probably damaging |
Het |
| Hmgcs2 |
T |
C |
3: 98,187,786 (GRCm39) |
|
probably benign |
Het |
| Ide |
T |
A |
19: 37,292,383 (GRCm39) |
I271L |
unknown |
Het |
| Kat8 |
G |
A |
7: 127,523,988 (GRCm39) |
E343K |
probably damaging |
Het |
| Kif14 |
A |
G |
1: 136,444,141 (GRCm39) |
I1378V |
probably benign |
Het |
| Lhx3 |
TCCTACGGGCCGGCCC |
TCC |
2: 26,091,435 (GRCm39) |
|
probably null |
Het |
| Lrp2 |
C |
T |
2: 69,319,502 (GRCm39) |
G2007D |
probably damaging |
Het |
| Lrp5 |
T |
C |
19: 3,709,304 (GRCm39) |
K142R |
probably damaging |
Het |
| Macroh2a1 |
C |
G |
13: 56,243,936 (GRCm39) |
|
probably null |
Het |
| Mrpl2 |
G |
A |
17: 46,960,964 (GRCm39) |
R286Q |
probably benign |
Het |
| Mtrfr |
A |
G |
5: 124,476,954 (GRCm39) |
N83D |
probably damaging |
Het |
| Nacad |
T |
A |
11: 6,548,528 (GRCm39) |
D1402V |
probably damaging |
Het |
| Ndfip2 |
T |
C |
14: 105,535,539 (GRCm39) |
I275T |
possibly damaging |
Het |
| Neb |
A |
C |
2: 52,116,582 (GRCm39) |
V4131G |
possibly damaging |
Het |
| Nfe2l1 |
G |
A |
11: 96,712,934 (GRCm39) |
A83V |
probably damaging |
Het |
| Nos3 |
A |
G |
5: 24,576,625 (GRCm39) |
D418G |
probably damaging |
Het |
| Or12e7 |
A |
T |
2: 87,288,138 (GRCm39) |
M210L |
probably benign |
Het |
| Or1n1b |
T |
A |
2: 36,780,056 (GRCm39) |
K268M |
possibly damaging |
Het |
| Plcd4 |
A |
G |
1: 74,604,313 (GRCm39) |
T764A |
probably damaging |
Het |
| Plppr3 |
G |
T |
10: 79,701,220 (GRCm39) |
P541T |
possibly damaging |
Het |
| Polr2a |
A |
G |
11: 69,637,771 (GRCm39) |
I191T |
possibly damaging |
Het |
| Pramel18 |
T |
C |
4: 101,766,436 (GRCm39) |
F40S |
probably damaging |
Het |
| Rab11fip1 |
T |
C |
8: 27,646,402 (GRCm39) |
K225E |
probably damaging |
Het |
| Rara |
A |
T |
11: 98,857,185 (GRCm39) |
Q64L |
possibly damaging |
Het |
| Rtkn |
G |
A |
6: 83,126,754 (GRCm39) |
V305M |
probably damaging |
Het |
| Sh2b1 |
A |
C |
7: 126,070,408 (GRCm39) |
F399V |
probably benign |
Het |
| Slc7a4 |
T |
C |
16: 17,393,482 (GRCm39) |
T106A |
probably damaging |
Het |
| Srcap |
G |
A |
7: 127,129,795 (GRCm39) |
G539D |
probably damaging |
Het |
| Stab1 |
C |
T |
14: 30,869,974 (GRCm39) |
|
probably null |
Het |
| Zfp267 |
G |
A |
3: 36,216,814 (GRCm39) |
C55Y |
possibly damaging |
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 |
|
R2393:Lhx6
|
UTSW |
2 |
35,981,402 (GRCm39) |
missense |
probably benign |
0.22 |
|
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'- TAGCCCATGCAAATGATGGAGC -3'
(R):5'- GCAGCCGATTTGGAACCAAG -3'
Sequencing Primer
(F):5'- AGCCAGAGCGCATGTTC -3'
(R):5'- ATTTGGAACCAAGTGCGCC -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation