Incidental Mutation 'R4379:Lmbr1l'
| ID |
325262 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lmbr1l
|
| Ensembl Gene |
ENSMUSG00000022999 |
| Gene Name |
limb region 1 like |
| Synonyms |
D15Ertd735e, 1110013E13Rik |
| MMRRC Submission |
041677-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4379 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
98801798-98815944 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
G to T
at 98807144 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Stop codon
at position 212
(C212*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000023736
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023736]
[ENSMUST00000109127]
|
| AlphaFold |
Q9D1E5 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000023736
AA Change: C212*
|
| SMART Domains |
Protein: ENSMUSP00000023736
Gene: ENSMUSG00000022999
AA Change: C212*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LMBR1
|
28 |
269 |
2e-41 |
PFAM |
|
Pfam:LMBR1
|
266 |
450 |
1.2e-35 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000109127
|
| SMART Domains |
Protein: ENSMUSP00000104755
Gene: ENSMUSG00000022999
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:LMBR1
|
1 |
324 |
6.3e-110 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123950
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127548
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128818
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135051
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231087
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.4%
|
| Validation Efficiency |
95% (53/56) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a gene disruption display normal morphology, clinical chemistry, hematology, and behavior. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1b |
C |
A |
5: 8,915,875 (GRCm39) |
H1252Q |
probably benign |
Het |
| Adcy3 |
T |
C |
12: 4,184,558 (GRCm39) |
L78P |
probably damaging |
Het |
| Agmat |
G |
T |
4: 141,484,802 (GRCm39) |
A282S |
probably benign |
Het |
| Akap8 |
G |
T |
17: 32,525,534 (GRCm39) |
T515K |
probably damaging |
Het |
| Akap8l |
T |
C |
17: 32,540,488 (GRCm39) |
|
probably benign |
Het |
| Alpk1 |
C |
T |
3: 127,523,022 (GRCm39) |
V7M |
probably damaging |
Het |
| AW209491 |
T |
C |
13: 14,812,412 (GRCm39) |
*422Q |
probably null |
Het |
| Cdan1 |
A |
G |
2: 120,557,099 (GRCm39) |
F576L |
probably damaging |
Het |
| Cers5 |
A |
G |
15: 99,649,134 (GRCm39) |
F45L |
probably damaging |
Het |
| Dst |
A |
G |
1: 34,267,056 (GRCm39) |
I5011V |
probably benign |
Het |
| Dst |
T |
C |
1: 34,202,316 (GRCm39) |
S215P |
probably damaging |
Het |
| En1 |
A |
G |
1: 120,531,084 (GRCm39) |
N108S |
possibly damaging |
Het |
| Entrep3 |
A |
T |
3: 89,093,064 (GRCm39) |
D274V |
probably damaging |
Het |
| Fancd2 |
T |
C |
6: 113,538,677 (GRCm39) |
S591P |
probably benign |
Het |
| Glt1d1 |
T |
C |
5: 127,771,346 (GRCm39) |
V279A |
possibly damaging |
Het |
| Gm10051 |
C |
T |
5: 133,504,287 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr158 |
G |
T |
2: 21,830,025 (GRCm39) |
G690V |
probably damaging |
Het |
| Grm7 |
G |
T |
6: 110,623,309 (GRCm39) |
V161F |
probably damaging |
Het |
| Grm7 |
T |
A |
6: 111,223,335 (GRCm39) |
N458K |
probably benign |
Het |
| Hibadh |
G |
A |
6: 52,597,027 (GRCm39) |
S139L |
probably damaging |
Het |
| Hivep1 |
C |
T |
13: 42,308,906 (GRCm39) |
S382F |
probably damaging |
Het |
| Ift74 |
A |
G |
4: 94,568,171 (GRCm39) |
N403D |
probably benign |
Het |
| Igkv4-81 |
A |
G |
6: 68,967,933 (GRCm39) |
L56S |
probably damaging |
Het |
| Igsf9b |
G |
A |
9: 27,220,774 (GRCm39) |
V47I |
possibly damaging |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lrp10 |
C |
T |
14: 54,705,823 (GRCm39) |
R338C |
probably damaging |
Het |
| Lrrc34 |
A |
G |
3: 30,685,524 (GRCm39) |
L275P |
probably damaging |
Het |
| Mgam2-ps |
T |
C |
6: 40,810,793 (GRCm39) |
|
noncoding transcript |
Het |
| Mief1 |
T |
G |
15: 80,132,160 (GRCm39) |
M77R |
possibly damaging |
Het |
| Neurod6 |
T |
C |
6: 55,656,257 (GRCm39) |
T127A |
probably damaging |
Het |
| Nif3l1 |
A |
C |
1: 58,494,738 (GRCm39) |
|
probably benign |
Het |
| Nlrp12 |
T |
A |
7: 3,288,554 (GRCm39) |
T653S |
probably benign |
Het |
| Nol7 |
G |
T |
13: 43,555,051 (GRCm39) |
W228L |
probably damaging |
Het |
| Nrp1 |
G |
A |
8: 129,194,948 (GRCm39) |
R468H |
probably damaging |
Het |
| Or5ac15 |
C |
T |
16: 58,940,027 (GRCm39) |
M135I |
probably benign |
Het |
| Or7g34 |
A |
G |
9: 19,478,038 (GRCm39) |
L211P |
probably benign |
Het |
| Pbrm1 |
A |
T |
14: 30,789,663 (GRCm39) |
H785L |
probably damaging |
Het |
| Pus7 |
T |
C |
5: 23,953,864 (GRCm39) |
|
probably benign |
Het |
| Qser1 |
G |
T |
2: 104,596,404 (GRCm39) |
|
probably null |
Het |
| Rrm1 |
T |
C |
7: 102,095,800 (GRCm39) |
V51A |
probably damaging |
Het |
| Setbp1 |
T |
C |
18: 79,129,896 (GRCm39) |
N112S |
probably damaging |
Het |
| Svil |
C |
T |
18: 5,046,909 (GRCm39) |
H52Y |
probably damaging |
Het |
| Taf1d |
T |
A |
9: 15,223,277 (GRCm39) |
|
probably benign |
Het |
| Tle1 |
ACAGGTTTCTTCAGGTTTCTT |
ACAGGTTTCTT |
4: 72,036,400 (GRCm39) |
|
probably benign |
Het |
| Treml1 |
A |
G |
17: 48,667,424 (GRCm39) |
Y103C |
probably damaging |
Het |
| Trim28 |
A |
T |
7: 12,763,407 (GRCm39) |
D516V |
probably damaging |
Het |
| Usp34 |
T |
A |
11: 23,334,499 (GRCm39) |
N1164K |
possibly damaging |
Het |
| Vmn2r115 |
A |
G |
17: 23,564,197 (GRCm39) |
Y123C |
possibly damaging |
Het |
| Vrk3 |
C |
T |
7: 44,424,866 (GRCm39) |
T427M |
probably benign |
Het |
| Zfp28 |
C |
T |
7: 6,396,441 (GRCm39) |
T292I |
probably benign |
Het |
| Zmynd8 |
A |
T |
2: 165,649,858 (GRCm39) |
|
probably null |
Het |
| Zscan4d |
A |
G |
7: 10,898,905 (GRCm39) |
V124A |
probably benign |
Het |
|
| Other mutations in Lmbr1l |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02002:Lmbr1l
|
APN |
15 |
98,802,666 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02097:Lmbr1l
|
APN |
15 |
98,815,772 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02731:Lmbr1l
|
APN |
15 |
98,815,777 (GRCm39) |
missense |
probably damaging |
0.96 |
|
finch
|
UTSW |
15 |
98,807,267 (GRCm39) |
critical splice donor site |
probably null |
|
|
Gooseberry
|
UTSW |
15 |
98,810,308 (GRCm39) |
missense |
probably damaging |
0.99 |
|
junco
|
UTSW |
15 |
98,810,408 (GRCm39) |
missense |
probably damaging |
1.00 |
|
morula
|
UTSW |
15 |
98,802,672 (GRCm39) |
missense |
probably damaging |
1.00 |
|
munia
|
UTSW |
15 |
98,807,150 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
strawberry
|
UTSW |
15 |
98,807,144 (GRCm39) |
nonsense |
probably null |
|
|
R0310:Lmbr1l
|
UTSW |
15 |
98,806,654 (GRCm39) |
splice site |
probably benign |
|
|
R1778:Lmbr1l
|
UTSW |
15 |
98,810,357 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2418:Lmbr1l
|
UTSW |
15 |
98,805,418 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R2419:Lmbr1l
|
UTSW |
15 |
98,805,418 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R4181:Lmbr1l
|
UTSW |
15 |
98,806,601 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R4472:Lmbr1l
|
UTSW |
15 |
98,804,178 (GRCm39) |
missense |
probably benign |
0.02 |
|
R5290:Lmbr1l
|
UTSW |
15 |
98,810,123 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5410:Lmbr1l
|
UTSW |
15 |
98,807,143 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5436:Lmbr1l
|
UTSW |
15 |
98,802,672 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5667:Lmbr1l
|
UTSW |
15 |
98,805,489 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R5671:Lmbr1l
|
UTSW |
15 |
98,805,489 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R5918:Lmbr1l
|
UTSW |
15 |
98,810,308 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6735:Lmbr1l
|
UTSW |
15 |
98,807,121 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6882:Lmbr1l
|
UTSW |
15 |
98,805,467 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7131:Lmbr1l
|
UTSW |
15 |
98,804,204 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7136:Lmbr1l
|
UTSW |
15 |
98,809,372 (GRCm39) |
splice site |
probably null |
|
|
R7169:Lmbr1l
|
UTSW |
15 |
98,807,075 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R7169:Lmbr1l
|
UTSW |
15 |
98,807,039 (GRCm39) |
frame shift |
probably null |
|
|
R7336:Lmbr1l
|
UTSW |
15 |
98,811,468 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7541:Lmbr1l
|
UTSW |
15 |
98,807,267 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7603:Lmbr1l
|
UTSW |
15 |
98,806,572 (GRCm39) |
nonsense |
probably null |
|
|
R7974:Lmbr1l
|
UTSW |
15 |
98,809,500 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8354:Lmbr1l
|
UTSW |
15 |
98,810,357 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8454:Lmbr1l
|
UTSW |
15 |
98,810,357 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8504:Lmbr1l
|
UTSW |
15 |
98,810,065 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8933:Lmbr1l
|
UTSW |
15 |
98,807,150 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R8974:Lmbr1l
|
UTSW |
15 |
98,810,408 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCATGTGCCGCACCTATTAGTG -3'
(R):5'- AAATAACGGGTTTCTGGTTCCTAG -3'
Sequencing Primer
(F):5'- AGTGCTACTCTCCATTAGTCCATTAG -3'
(R):5'- AACGGGTTTCTGGTTCCTAGTCTTG -3'
|
| Genotyping |
Genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the mutation (G>T @ 98,909,263 (assembly) in the Lmbr1l gene). PCR Primers
R43790046_PCR_F: 5’- TGTGTTCTGACCAACTCCAG-3’
R43790046_PCR_R: 5’- GCAAGACAAGTTGACATGGC-3’ Sequencing Primers
R43790046_SEQ_F: 5’- GTGTTCTGACCAACTCCAGATGATG-3’
R43790046_SEQ_R: 5’- AGACTTCTGGGAGTACTACCTC-3’
PCR program
1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40X
6) 72°C 10:00
7) 4°C hold The following sequence of 460 nucleotides is amplified (NCBI RefSeq: NC_000081, chromosome 15): tgtgttctga ccaactccag atgatgggaa ggggtgctgg ggtgggggtg gggggcaaca
acacagaagc caagcaaggg tgtggccttc aaatgtagga aattggccct gagcaagagg
cagggagcac tacatactac atactacata ctacatacta catactacat acccggggct
tgaccagcaa cttcccagtg acagagaaca tgcgggcgag acctagtgga gtgcacactg
taggcacaag agctggtcag tcacatgcca gacctttcac tccctcccca cacctcctcc
ttccaccctg actgatgccc acgatgccct cttcctctcc cagattctga cactcaccca
gaagcagcag aactccgagg aaggagatac aggagtagag ataggggagg tagtactccc
agaagtctag gacaataaaa gccatgtcaa cttgtcttgc Primer binding sites are underlined and the sequencing primer is highlighted; the mutated nucleotide is shown in red text (Chr. (+) = G>T; sense strand = C>A)
|
| Posted On |
2015-07-06 |
Incidental Mutation