Incidental Mutation 'R0968:Lca5'
| ID |
83953 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lca5
|
| Ensembl Gene |
ENSMUSG00000032258 |
| Gene Name |
Leber congenital amaurosis 5 (human) |
| Synonyms |
4930431B11Rik, ORF64, 5730406O13Rik |
| MMRRC Submission |
039097-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.454)
|
| Stock # |
R0968 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
83272346-83323180 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 83305222 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 195
(T195A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000034791
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034791]
[ENSMUST00000034793]
[ENSMUST00000186802]
[ENSMUST00000188548]
[ENSMUST00000190514]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000034791
AA Change: T195A
PolyPhen 2
Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000034791
Gene: ENSMUSG00000032258
AA Change: T195A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
40 |
N/A |
INTRINSIC |
|
Pfam:Lebercilin
|
103 |
295 |
2.6e-66 |
PFAM |
|
low complexity region
|
306 |
315 |
N/A |
INTRINSIC |
|
low complexity region
|
617 |
627 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000034793
AA Change: T195A
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000034793
Gene: ENSMUSG00000032258
AA Change: T195A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
40 |
N/A |
INTRINSIC |
|
Pfam:Lebercilin
|
102 |
295 |
4.8e-71 |
PFAM |
|
low complexity region
|
306 |
315 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000186802
|
| SMART Domains |
Protein: ENSMUSP00000139529
Gene: ENSMUSG00000032258
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
40 |
N/A |
INTRINSIC |
|
Pfam:Lebercilin
|
102 |
176 |
1e-29 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000188548
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000188907
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000190373
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000190514
AA Change: T195A
PolyPhen 2
Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
|
| SMART Domains |
Protein: ENSMUSP00000140753
Gene: ENSMUSG00000032258
AA Change: T195A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
25 |
40 |
N/A |
INTRINSIC |
|
Pfam:Lebercilin
|
102 |
295 |
5.8e-71 |
PFAM |
|
low complexity region
|
306 |
315 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000190557
|
| Meta Mutation Damage Score |
0.0589 |
| Coding Region Coverage |
- 1x: 99.5%
- 3x: 99.0%
- 10x: 98.0%
- 20x: 96.7%
|
| Validation Efficiency |
94% (34/36) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is thought to be involved in centrosomal or ciliary functions. Mutations in this gene cause Leber congenital amaurosis type V. Alternatively spliced transcript variants are described. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit retinal patches of depigmentation, lack rod and cone ERG responses to light stimuli, and show loss of ciliary intraflagellar transport function in photoreceptors leading to failure of outer segment formation and photoreceptor degeneration. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
G |
A |
3: 137,772,967 (GRCm39) |
V719M |
probably damaging |
Het |
| Abca13 |
A |
G |
11: 9,248,016 (GRCm39) |
S2588G |
probably benign |
Het |
| Acaca |
C |
T |
11: 84,129,859 (GRCm39) |
Q405* |
probably null |
Het |
| Brms1l |
G |
A |
12: 55,912,798 (GRCm39) |
D264N |
possibly damaging |
Het |
| Cabcoco1 |
T |
C |
10: 68,272,202 (GRCm39) |
M254V |
probably benign |
Het |
| Cndp1 |
G |
A |
18: 84,652,777 (GRCm39) |
|
probably benign |
Het |
| Coro7 |
G |
C |
16: 4,487,919 (GRCm39) |
|
probably benign |
Het |
| Cylc2 |
A |
G |
4: 51,216,706 (GRCm39) |
M1V |
probably null |
Het |
| Cyp3a11 |
G |
A |
5: 145,799,324 (GRCm39) |
|
probably benign |
Het |
| Dnah10 |
C |
T |
5: 124,906,641 (GRCm39) |
T4224M |
probably damaging |
Het |
| Dnah2 |
T |
C |
11: 69,339,345 (GRCm39) |
E3054G |
possibly damaging |
Het |
| Dnm3 |
A |
G |
1: 161,847,388 (GRCm39) |
|
probably benign |
Het |
| Efcab5 |
G |
A |
11: 77,031,749 (GRCm39) |
R42W |
probably damaging |
Het |
| Fgf12 |
T |
C |
16: 27,981,185 (GRCm39) |
N177S |
probably null |
Het |
| Flt3 |
C |
T |
5: 147,278,037 (GRCm39) |
V846I |
possibly damaging |
Het |
| Gm11569 |
A |
T |
11: 99,689,250 (GRCm39) |
|
probably benign |
Het |
| Gm12695 |
A |
C |
4: 96,650,303 (GRCm39) |
V181G |
probably damaging |
Het |
| Gtf3c3 |
C |
T |
1: 54,456,937 (GRCm39) |
A488T |
probably damaging |
Het |
| Lars1 |
C |
A |
18: 42,351,648 (GRCm39) |
R852L |
probably benign |
Het |
| Lrrc40 |
G |
A |
3: 157,742,426 (GRCm39) |
D14N |
probably damaging |
Het |
| Map4k2 |
T |
C |
19: 6,395,487 (GRCm39) |
S327P |
probably damaging |
Het |
| Mpp4 |
A |
G |
1: 59,169,249 (GRCm39) |
F397L |
probably damaging |
Het |
| Mtus2 |
T |
C |
5: 148,014,994 (GRCm39) |
S596P |
probably benign |
Het |
| Myo3a |
T |
A |
2: 22,448,301 (GRCm39) |
N25K |
probably damaging |
Het |
| Nadsyn1 |
T |
C |
7: 143,359,770 (GRCm39) |
T401A |
probably benign |
Het |
| Pde6a |
A |
T |
18: 61,386,809 (GRCm39) |
E395D |
probably damaging |
Het |
| Plekhm2 |
A |
G |
4: 141,357,243 (GRCm39) |
V743A |
probably benign |
Het |
| Pzp |
A |
T |
6: 128,502,108 (GRCm39) |
D80E |
probably benign |
Het |
| Rp1 |
A |
T |
1: 4,415,575 (GRCm39) |
C1846S |
probably benign |
Het |
| Shbg |
A |
G |
11: 69,508,014 (GRCm39) |
L117P |
probably damaging |
Het |
| Slc35e1 |
T |
C |
8: 73,246,415 (GRCm39) |
|
probably benign |
Het |
| Slc5a2 |
G |
C |
7: 127,869,803 (GRCm39) |
R412P |
probably damaging |
Het |
| Sned1 |
G |
A |
1: 93,209,376 (GRCm39) |
V830M |
possibly damaging |
Het |
| Supt20 |
A |
G |
3: 54,615,821 (GRCm39) |
|
probably benign |
Het |
| Vcpip1 |
A |
T |
1: 9,816,604 (GRCm39) |
I593N |
probably damaging |
Het |
|
| Other mutations in Lca5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01073:Lca5
|
APN |
9 |
83,277,528 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL01349:Lca5
|
APN |
9 |
83,308,670 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01918:Lca5
|
APN |
9 |
83,305,201 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02035:Lca5
|
APN |
9 |
83,305,365 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02276:Lca5
|
APN |
9 |
83,280,638 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
IGL02425:Lca5
|
APN |
9 |
83,281,774 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02481:Lca5
|
APN |
9 |
83,305,170 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02483:Lca5
|
APN |
9 |
83,305,170 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0465:Lca5
|
UTSW |
9 |
83,277,920 (GRCm39) |
nonsense |
probably null |
|
|
R0610:Lca5
|
UTSW |
9 |
83,281,792 (GRCm39) |
missense |
probably benign |
0.24 |
|
R0811:Lca5
|
UTSW |
9 |
83,281,806 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0812:Lca5
|
UTSW |
9 |
83,281,806 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R1891:Lca5
|
UTSW |
9 |
83,277,661 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5223:Lca5
|
UTSW |
9 |
83,280,666 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5235:Lca5
|
UTSW |
9 |
83,305,107 (GRCm39) |
nonsense |
probably null |
|
|
R5260:Lca5
|
UTSW |
9 |
83,305,276 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5531:Lca5
|
UTSW |
9 |
83,280,648 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5558:Lca5
|
UTSW |
9 |
83,283,796 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5688:Lca5
|
UTSW |
9 |
83,280,619 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5886:Lca5
|
UTSW |
9 |
83,281,734 (GRCm39) |
missense |
probably benign |
0.31 |
|
R6426:Lca5
|
UTSW |
9 |
83,277,707 (GRCm39) |
nonsense |
probably null |
|
|
R7108:Lca5
|
UTSW |
9 |
83,305,222 (GRCm39) |
missense |
probably benign |
0.25 |
|
R7151:Lca5
|
UTSW |
9 |
83,280,693 (GRCm39) |
missense |
probably benign |
0.20 |
|
R7314:Lca5
|
UTSW |
9 |
83,277,563 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R7378:Lca5
|
UTSW |
9 |
83,277,583 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7468:Lca5
|
UTSW |
9 |
83,305,509 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7686:Lca5
|
UTSW |
9 |
83,277,292 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8874:Lca5
|
UTSW |
9 |
83,277,503 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8934:Lca5
|
UTSW |
9 |
83,273,909 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R8987:Lca5
|
UTSW |
9 |
83,283,796 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGAGCTGCAATGGGCTACTCAATC -3'
(R):5'- CCTTCAGTATCGTCAGGAGAAAGCG -3'
Sequencing Primer
(F):5'- GGCTACTCAATCAGAGTCCC -3'
(R):5'- GCGCTGAATAAGTTTGAAGATGC -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation