Incidental Mutation 'R0314:Limd1'
| ID |
25378 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Limd1
|
| Ensembl Gene |
ENSMUSG00000025239 |
| Gene Name |
LIM domains containing 1 |
| Synonyms |
D9Ertd192e |
| MMRRC Submission |
038524-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.340)
|
| Stock # |
R0314 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
123307771-123350617 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 123345892 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Serine
at position 557
(I557S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000026269
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026269]
|
| AlphaFold |
Q9QXD8 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026269
AA Change: I557S
PolyPhen 2
Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: I557S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
57 |
67 |
N/A |
INTRINSIC |
|
low complexity region
|
238 |
252 |
N/A |
INTRINSIC |
|
LIM
|
463 |
516 |
2.17e-15 |
SMART |
|
LIM
|
528 |
580 |
9.6e-17 |
SMART |
|
LIM
|
588 |
649 |
2.26e-13 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000213278
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000214309
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000216352
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000217639
|
| Meta Mutation Damage Score |
0.1889 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.8%
- 10x: 94.9%
- 20x: 88.7%
|
| Validation Efficiency |
100% (41/41) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal basal bone osteoclast numbers and bone density but are resistant to physiological and pathologic osteoclastogenic stimuli. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arih2 |
T |
C |
9: 108,485,878 (GRCm39) |
N345D |
probably damaging |
Het |
| Ascc3 |
C |
T |
10: 50,514,095 (GRCm39) |
S298L |
possibly damaging |
Het |
| Cacna1e |
A |
G |
1: 154,317,997 (GRCm39) |
Y1462H |
probably damaging |
Het |
| Car9 |
T |
C |
4: 43,509,212 (GRCm39) |
|
probably null |
Het |
| Cenpc1 |
A |
T |
5: 86,185,230 (GRCm39) |
M427K |
probably benign |
Het |
| Chl1 |
T |
A |
6: 103,624,262 (GRCm39) |
C57S |
probably damaging |
Het |
| Cntn3 |
T |
C |
6: 102,397,342 (GRCm39) |
Y77C |
probably damaging |
Het |
| Cobll1 |
T |
C |
2: 64,919,865 (GRCm39) |
K1187E |
possibly damaging |
Het |
| Fkbpl |
C |
T |
17: 34,865,026 (GRCm39) |
H265Y |
possibly damaging |
Het |
| Fmo1 |
T |
G |
1: 162,687,031 (GRCm39) |
E32A |
probably damaging |
Het |
| Fnip2 |
G |
A |
3: 79,388,496 (GRCm39) |
T715I |
probably damaging |
Het |
| Fzd6 |
T |
A |
15: 38,889,128 (GRCm39) |
I82K |
possibly damaging |
Het |
| Grm5 |
T |
C |
7: 87,252,163 (GRCm39) |
S138P |
probably damaging |
Het |
| Klra5 |
T |
C |
6: 129,880,553 (GRCm39) |
Y115C |
probably damaging |
Het |
| Lgr4 |
T |
C |
2: 109,821,438 (GRCm39) |
|
probably benign |
Het |
| Mpv17l |
A |
T |
16: 13,758,863 (GRCm39) |
I96L |
probably benign |
Het |
| Neb |
A |
T |
2: 52,133,343 (GRCm39) |
D3398E |
probably benign |
Het |
| Nup155 |
T |
C |
15: 8,176,736 (GRCm39) |
S1005P |
probably benign |
Het |
| Or2v2 |
A |
T |
11: 49,004,519 (GRCm39) |
D11E |
possibly damaging |
Het |
| Or52a5b |
T |
C |
7: 103,417,388 (GRCm39) |
D72G |
probably damaging |
Het |
| Pebp4 |
G |
T |
14: 70,297,103 (GRCm39) |
S214I |
possibly damaging |
Het |
| Pex26 |
T |
C |
6: 121,161,443 (GRCm39) |
|
probably null |
Het |
| Rbbp8 |
A |
T |
18: 11,848,875 (GRCm39) |
Q230L |
probably benign |
Het |
| Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
| Robo2 |
G |
A |
16: 73,753,525 (GRCm39) |
T784M |
probably damaging |
Het |
| Slc5a1 |
T |
C |
5: 33,303,995 (GRCm39) |
I270T |
probably benign |
Het |
| Spag4 |
C |
T |
2: 155,909,229 (GRCm39) |
|
probably benign |
Het |
| Stt3a |
T |
C |
9: 36,660,841 (GRCm39) |
|
probably benign |
Het |
| Svep1 |
C |
T |
4: 58,096,331 (GRCm39) |
E1430K |
possibly damaging |
Het |
| Timd5 |
G |
A |
11: 46,419,364 (GRCm39) |
C60Y |
probably damaging |
Het |
| Uba6 |
A |
T |
5: 86,265,946 (GRCm39) |
V956E |
probably damaging |
Het |
| Ube2j1 |
T |
A |
4: 33,043,991 (GRCm39) |
|
probably benign |
Het |
| Ubr5 |
A |
G |
15: 37,997,431 (GRCm39) |
S1741P |
probably damaging |
Het |
| Vmn2r1 |
A |
G |
3: 63,993,980 (GRCm39) |
T109A |
probably damaging |
Het |
| Vmn2r60 |
T |
C |
7: 41,784,985 (GRCm39) |
|
probably benign |
Het |
| Vstm2a |
A |
G |
11: 16,318,388 (GRCm39) |
|
probably benign |
Het |
| Zdhhc20 |
T |
A |
14: 58,094,076 (GRCm39) |
K195N |
probably damaging |
Het |
| Zfp683 |
A |
G |
4: 133,786,052 (GRCm39) |
Y393C |
probably benign |
Het |
| Zzz3 |
T |
C |
3: 152,133,085 (GRCm39) |
S48P |
probably benign |
Het |
|
| Other mutations in Limd1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00953:Limd1
|
APN |
9 |
123,308,948 (GRCm39) |
missense |
probably benign |
0.31 |
|
IGL00972:Limd1
|
APN |
9 |
123,309,141 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL01815:Limd1
|
APN |
9 |
123,308,801 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02598:Limd1
|
APN |
9 |
123,309,236 (GRCm39) |
missense |
probably benign |
|
|
IGL02598:Limd1
|
APN |
9 |
123,345,933 (GRCm39) |
missense |
probably benign |
0.11 |
|
IGL02633:Limd1
|
APN |
9 |
123,308,987 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02999:Limd1
|
APN |
9 |
123,345,864 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1612:Limd1
|
UTSW |
9 |
123,347,219 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2009:Limd1
|
UTSW |
9 |
123,308,564 (GRCm39) |
missense |
probably benign |
|
|
R2299:Limd1
|
UTSW |
9 |
123,345,942 (GRCm39) |
nonsense |
probably null |
|
|
R3791:Limd1
|
UTSW |
9 |
123,309,439 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R4453:Limd1
|
UTSW |
9 |
123,309,359 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R5979:Limd1
|
UTSW |
9 |
123,308,479 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R7493:Limd1
|
UTSW |
9 |
123,308,748 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8101:Limd1
|
UTSW |
9 |
123,329,216 (GRCm39) |
nonsense |
probably null |
|
|
R8332:Limd1
|
UTSW |
9 |
123,308,319 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9060:Limd1
|
UTSW |
9 |
123,309,514 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9679:Limd1
|
UTSW |
9 |
123,308,457 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9681:Limd1
|
UTSW |
9 |
123,345,903 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R9726:Limd1
|
UTSW |
9 |
123,308,984 (GRCm39) |
missense |
probably benign |
0.00 |
|
X0028:Limd1
|
UTSW |
9 |
123,345,927 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1177:Limd1
|
UTSW |
9 |
123,309,086 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTGTTGGCACGTTCAAGCAGAC -3'
(R):5'- AATTATGTAAAGCTGGGGCCACAGG -3'
Sequencing Primer
(F):5'- GCTCCTCAACCAATGTGTTC -3'
(R):5'- AGGCTTGTTGAATTCCTCTGATTAC -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation