Incidental Mutation 'R6735:Lhx6'
| ID |
530166 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lhx6
|
| Ensembl Gene |
ENSMUSG00000026890 |
| Gene Name |
LIM homeobox protein 6 |
| Synonyms |
|
| MMRRC Submission |
044853-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.930)
|
| Stock # |
R6735 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
35971965-35995420 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 35981390 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Alanine
at position 67
(D67A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135776
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000112960]
[ENSMUST00000112961]
[ENSMUST00000112963]
[ENSMUST00000112966]
[ENSMUST00000112967]
[ENSMUST00000136821]
[ENSMUST00000148852]
|
| AlphaFold |
Q9R1R0 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000112960
AA Change: D274A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: D274A
| 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 |
possibly damaging
Transcript: ENSMUST00000112961
AA Change: D245A
PolyPhen 2
Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: D245A
| 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 |
possibly damaging
Transcript: ENSMUST00000112963
AA Change: D245A
PolyPhen 2
Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: D245A
| 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 |
possibly damaging
Transcript: ENSMUST00000112966
AA Change: D245A
PolyPhen 2
Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: D245A
| 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 |
possibly damaging
Transcript: ENSMUST00000112967
AA Change: D274A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: D274A
| 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 damaging
Transcript: ENSMUST00000136821
AA Change: D67A
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000135776
Gene: ENSMUSG00000026890
AA Change: D67A
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
10 |
64 |
3.17e-17 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000148852
AA Change: D245A
PolyPhen 2
Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: D245A
| 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 |
0.3936 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.3%
- 20x: 95.5%
|
| Validation Efficiency |
100% (47/47) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2510039O18Rik |
A |
G |
4: 148,026,274 (GRCm39) |
T265A |
probably benign |
Het |
| Adap1 |
A |
T |
5: 139,278,900 (GRCm39) |
Y127N |
probably damaging |
Het |
| Alg8 |
T |
C |
7: 97,032,189 (GRCm39) |
F246S |
probably benign |
Het |
| Alpk1 |
A |
G |
3: 127,518,098 (GRCm39) |
Y68H |
probably damaging |
Het |
| Arhgef5 |
T |
C |
6: 43,251,966 (GRCm39) |
S906P |
probably benign |
Het |
| C9 |
A |
T |
15: 6,519,387 (GRCm39) |
D408V |
probably benign |
Het |
| Cnot2 |
G |
A |
10: 116,334,058 (GRCm39) |
P371S |
possibly damaging |
Het |
| Cpeb4 |
T |
A |
11: 31,874,700 (GRCm39) |
Y174N |
probably benign |
Het |
| Enpp3 |
A |
G |
10: 24,683,351 (GRCm39) |
Y289H |
probably damaging |
Het |
| Erbin |
A |
T |
13: 104,020,718 (GRCm39) |
D80E |
probably damaging |
Het |
| Fgd6 |
A |
T |
10: 93,910,182 (GRCm39) |
E829V |
possibly damaging |
Het |
| Foxn2 |
T |
G |
17: 88,794,223 (GRCm39) |
S387A |
probably benign |
Het |
| Hapstr1 |
T |
A |
16: 8,673,764 (GRCm39) |
H230Q |
probably benign |
Het |
| Irag2 |
T |
C |
6: 145,106,619 (GRCm39) |
L201S |
probably damaging |
Het |
| Kif13a |
A |
G |
13: 46,906,222 (GRCm39) |
S574P |
possibly damaging |
Het |
| Lmbr1l |
A |
T |
15: 98,807,121 (GRCm39) |
M220K |
probably damaging |
Het |
| Macroh2a2 |
A |
G |
10: 61,577,046 (GRCm39) |
I274T |
probably damaging |
Het |
| Naa35 |
T |
C |
13: 59,773,378 (GRCm39) |
L111P |
probably damaging |
Het |
| Notch2 |
T |
A |
3: 98,041,902 (GRCm39) |
V1307E |
probably damaging |
Het |
| Nts |
T |
A |
10: 102,320,859 (GRCm39) |
M77L |
probably benign |
Het |
| Or5m11b |
A |
C |
2: 85,805,778 (GRCm39) |
S64R |
possibly damaging |
Het |
| Pigz |
A |
G |
16: 31,764,361 (GRCm39) |
N473S |
probably benign |
Het |
| Pkd2 |
A |
G |
5: 104,628,195 (GRCm39) |
D423G |
probably damaging |
Het |
| Plac8 |
A |
G |
5: 100,710,485 (GRCm39) |
|
probably null |
Het |
| Ppp2r2b |
T |
C |
18: 42,821,653 (GRCm39) |
|
probably null |
Het |
| Proc |
T |
C |
18: 32,256,701 (GRCm39) |
N322S |
probably benign |
Het |
| Prpf40b |
C |
T |
15: 99,212,784 (GRCm39) |
R627W |
probably damaging |
Het |
| Psd3 |
A |
G |
8: 68,573,398 (GRCm39) |
|
probably null |
Het |
| Safb |
A |
G |
17: 56,892,169 (GRCm39) |
|
probably benign |
Het |
| Scnn1g |
A |
G |
7: 121,341,486 (GRCm39) |
D216G |
probably benign |
Het |
| Septin7 |
A |
G |
9: 25,215,048 (GRCm39) |
E345G |
possibly damaging |
Het |
| Sult2a5 |
A |
T |
7: 13,398,983 (GRCm39) |
K197* |
probably null |
Het |
| Suv39h1 |
C |
A |
X: 7,929,138 (GRCm39) |
R397L |
probably damaging |
Homo |
| Thbs4 |
T |
A |
13: 92,891,674 (GRCm39) |
M814L |
possibly damaging |
Het |
| Tmem14a |
T |
A |
1: 21,299,805 (GRCm39) |
|
probably benign |
Het |
| Tmprss11d |
C |
A |
5: 86,457,159 (GRCm39) |
A167S |
probably damaging |
Het |
| Ttn |
C |
A |
2: 76,629,252 (GRCm39) |
C14362F |
probably damaging |
Het |
| Usp15 |
T |
C |
10: 123,004,272 (GRCm39) |
I161V |
possibly damaging |
Het |
| Vmn1r67 |
T |
C |
7: 10,181,138 (GRCm39) |
L134P |
probably damaging |
Het |
| Wdr74 |
A |
G |
19: 8,713,586 (GRCm39) |
E73G |
possibly damaging |
Het |
| Zbtb49 |
A |
T |
5: 38,358,402 (GRCm39) |
M617K |
possibly damaging |
Het |
| Zc3h3 |
G |
A |
15: 75,628,483 (GRCm39) |
T937I |
probably benign |
Het |
| Zeb2 |
C |
T |
2: 45,000,028 (GRCm39) |
V25M |
probably null |
Het |
| Zfp108 |
T |
C |
7: 23,961,197 (GRCm39) |
F596S |
probably damaging |
Het |
| Zfyve1 |
T |
A |
12: 83,641,618 (GRCm39) |
N13Y |
possibly damaging |
Het |
| Zswim2 |
T |
C |
2: 83,754,105 (GRCm39) |
D185G |
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 |
|
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 |
|
|
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'- CTGCACTCTCAGTAATCAAGGAAAAG -3'
(R):5'- TGTTCGGGACTTGTGACTCC -3'
Sequencing Primer
(F):5'- GGGTCCTTAGGCCACACTG -3'
(R):5'- GACTTGTGACTCCGCCCC -3'
|
| Posted On |
2018-08-01 |
Incidental Mutation