Incidental Mutation 'R5105:Large1'
| ID |
401990 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Large1
|
| Ensembl Gene |
ENSMUSG00000004383 |
| Gene Name |
LARGE xylosyl- and glucuronyltransferase 1 |
| Synonyms |
froggy, enr, BPFD#36, fg |
| MMRRC Submission |
042693-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.586)
|
| Stock # |
R5105 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
73541227-74080164 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
A to T
at 73578872 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Stop codon
at position 444
(Y444*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000148336
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004497]
[ENSMUST00000119826]
[ENSMUST00000212459]
|
| AlphaFold |
Q9Z1M7 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000004497
AA Change: Y444*
|
| SMART Domains |
Protein: ENSMUSP00000004497
Gene: ENSMUSG00000004383
AA Change: Y444*
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
12 |
34 |
N/A |
INTRINSIC |
|
coiled coil region
|
55 |
90 |
N/A |
INTRINSIC |
|
Pfam:Glyco_transf_8
|
141 |
387 |
6.2e-22 |
PFAM |
|
Pfam:Glyco_transf_49
|
473 |
540 |
5.2e-15 |
PFAM |
|
Pfam:Glyco_transf_49
|
535 |
743 |
1.1e-47 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000119826
AA Change: Y444*
|
| SMART Domains |
Protein: ENSMUSP00000112617
Gene: ENSMUSG00000004383
AA Change: Y444*
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
12 |
34 |
N/A |
INTRINSIC |
|
coiled coil region
|
55 |
90 |
N/A |
INTRINSIC |
|
Pfam:Glyco_transf_8
|
142 |
386 |
3e-23 |
PFAM |
|
Pfam:Glyco_transf_49
|
473 |
540 |
2.3e-11 |
PFAM |
|
Pfam:Glyco_transf_49
|
520 |
743 |
2.7e-44 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000212459
AA Change: Y444*
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.8%
|
| Validation Efficiency |
96% (52/54) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene, which is one of the largest in the human genome, encodes a member of the N-acetylglucosaminyltransferase gene family. It encodes a glycosyltransferase which participates in glycosylation of alpha-dystroglycan, and may carry out the synthesis of glycoprotein and glycosphingolipid sugar chains. It may also be involved in the addition of a repeated disaccharide unit. Mutations in this gene cause MDC1D, a novel form of congenital muscular dystrophy with severe mental retardation and abnormal glycosylation of alpha-dystroglycan. Alternative splicing of this gene results in two transcript variants that encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes exhibit a progressive myopathy, abnormal posture, thoracic kyphosis, calcium deposits in muscle, loss of Schwann cells and myelin, eye and CNS defects, deafness, reduced growth, and death around 4 months. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Btbd8 |
T |
G |
5: 107,658,337 (GRCm39) |
S1124A |
possibly damaging |
Het |
| Camsap1 |
A |
G |
2: 25,830,941 (GRCm39) |
S445P |
probably damaging |
Het |
| Ccdc92 |
G |
A |
5: 124,912,858 (GRCm39) |
P224S |
probably damaging |
Het |
| Cep135 |
T |
C |
5: 76,741,939 (GRCm39) |
V125A |
probably benign |
Het |
| Cep192 |
T |
A |
18: 67,999,612 (GRCm39) |
C2159S |
probably benign |
Het |
| Col1a1 |
G |
T |
11: 94,833,211 (GRCm39) |
R404L |
unknown |
Het |
| Col6a3 |
A |
T |
1: 90,725,862 (GRCm39) |
M1382K |
possibly damaging |
Het |
| Cyp4a12b |
T |
C |
4: 115,290,958 (GRCm39) |
S329P |
probably damaging |
Het |
| Dclk1 |
T |
G |
3: 55,163,360 (GRCm39) |
S151A |
probably benign |
Het |
| Ddhd1 |
A |
T |
14: 45,894,864 (GRCm39) |
V202E |
probably benign |
Het |
| Dlx6 |
AGG |
AG |
6: 6,865,180 (GRCm39) |
|
probably null |
Het |
| Dnah10 |
A |
G |
5: 124,888,546 (GRCm39) |
E3050G |
probably benign |
Het |
| Dync1h1 |
T |
A |
12: 110,584,366 (GRCm39) |
F590I |
probably damaging |
Het |
| Eif4b |
T |
C |
15: 101,992,631 (GRCm39) |
Y63H |
probably benign |
Het |
| Fscb |
T |
C |
12: 64,520,110 (GRCm39) |
E452G |
possibly damaging |
Het |
| Gpx3 |
A |
T |
11: 54,797,980 (GRCm39) |
T39S |
possibly damaging |
Het |
| Grin2b |
T |
A |
6: 135,709,439 (GRCm39) |
Y1369F |
probably benign |
Het |
| Kank4 |
A |
T |
4: 98,667,396 (GRCm39) |
N350K |
probably benign |
Het |
| Kdm5d |
A |
G |
Y: 941,752 (GRCm39) |
K1318E |
probably benign |
Het |
| Lhx3 |
TCCTACGGGCCGGCCC |
TCC |
2: 26,091,435 (GRCm39) |
|
probably null |
Het |
| Lrrc47 |
A |
G |
4: 154,096,673 (GRCm39) |
Q156R |
probably damaging |
Het |
| Lrriq4 |
T |
C |
3: 30,704,632 (GRCm39) |
L220P |
probably damaging |
Het |
| Matn2 |
A |
G |
15: 34,355,814 (GRCm39) |
D273G |
possibly damaging |
Het |
| Myo18b |
T |
A |
5: 112,988,644 (GRCm39) |
I981F |
probably damaging |
Het |
| Or1q1 |
G |
A |
2: 36,887,469 (GRCm39) |
|
probably null |
Het |
| Or2n1c |
A |
C |
17: 38,519,208 (GRCm39) |
E24A |
possibly damaging |
Het |
| Or5aq1 |
A |
G |
2: 86,966,554 (GRCm39) |
I37T |
probably benign |
Het |
| Or6b13 |
A |
G |
7: 139,782,462 (GRCm39) |
Y74H |
probably damaging |
Het |
| Or8d6 |
T |
C |
9: 39,853,694 (GRCm39) |
V46A |
probably benign |
Het |
| Pkdrej |
T |
C |
15: 85,700,585 (GRCm39) |
T1784A |
probably damaging |
Het |
| Ppp3cb |
A |
G |
14: 20,559,490 (GRCm39) |
V422A |
possibly damaging |
Het |
| Rlf |
G |
A |
4: 121,007,564 (GRCm39) |
T472I |
probably damaging |
Het |
| Scaf11 |
T |
C |
15: 96,318,313 (GRCm39) |
E417G |
probably damaging |
Het |
| Shisa2 |
A |
T |
14: 59,867,263 (GRCm39) |
T172S |
possibly damaging |
Het |
| Siglec1 |
T |
A |
2: 130,922,320 (GRCm39) |
Q585L |
possibly damaging |
Het |
| Sorcs1 |
A |
T |
19: 50,213,579 (GRCm39) |
M716K |
possibly damaging |
Het |
| Sparcl1 |
C |
T |
5: 104,233,629 (GRCm39) |
M573I |
probably damaging |
Het |
| Stxbp5l |
C |
A |
16: 36,962,734 (GRCm39) |
V774F |
probably benign |
Het |
| Tcaf3 |
A |
G |
6: 42,568,259 (GRCm39) |
F699S |
probably damaging |
Het |
| Tmem87b |
T |
C |
2: 128,673,509 (GRCm39) |
V251A |
probably damaging |
Het |
| Trpc6 |
T |
A |
9: 8,649,471 (GRCm39) |
N560K |
probably benign |
Het |
| Trpv4 |
T |
A |
5: 114,764,981 (GRCm39) |
I678F |
probably damaging |
Het |
| Ttc3 |
A |
T |
16: 94,267,793 (GRCm39) |
H1935L |
possibly damaging |
Het |
| Vmn2r59 |
T |
A |
7: 41,696,529 (GRCm39) |
Y71F |
probably benign |
Het |
| Wdfy3 |
A |
G |
5: 102,003,415 (GRCm39) |
I2900T |
probably damaging |
Het |
| Zfp184 |
A |
G |
13: 22,143,799 (GRCm39) |
T502A |
possibly damaging |
Het |
| Zmym6 |
A |
G |
4: 127,017,551 (GRCm39) |
I1019V |
probably benign |
Het |
|
| Other mutations in Large1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00095:Large1
|
APN |
8 |
73,564,125 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00326:Large1
|
APN |
8 |
73,858,611 (GRCm39) |
missense |
probably benign |
|
|
IGL00418:Large1
|
APN |
8 |
73,550,469 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL01155:Large1
|
APN |
8 |
73,858,617 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01793:Large1
|
APN |
8 |
73,585,809 (GRCm39) |
splice site |
probably benign |
|
|
IGL01929:Large1
|
APN |
8 |
73,585,903 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02218:Large1
|
APN |
8 |
73,638,750 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02276:Large1
|
APN |
8 |
73,544,721 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02329:Large1
|
APN |
8 |
73,774,945 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
IGL02543:Large1
|
APN |
8 |
73,775,042 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02887:Large1
|
APN |
8 |
73,858,667 (GRCm39) |
missense |
probably benign |
0.07 |
|
biggs
|
UTSW |
8 |
73,843,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
umber
|
UTSW |
8 |
73,609,892 (GRCm39) |
nonsense |
probably null |
|
|
R0179:Large1
|
UTSW |
8 |
73,825,474 (GRCm39) |
missense |
probably benign |
0.09 |
|
R0477:Large1
|
UTSW |
8 |
73,544,710 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0587:Large1
|
UTSW |
8 |
73,585,961 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0791:Large1
|
UTSW |
8 |
73,775,107 (GRCm39) |
splice site |
probably benign |
|
|
R1253:Large1
|
UTSW |
8 |
73,775,050 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1695:Large1
|
UTSW |
8 |
73,544,710 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2017:Large1
|
UTSW |
8 |
73,578,825 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4835:Large1
|
UTSW |
8 |
73,774,975 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5120:Large1
|
UTSW |
8 |
73,585,969 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5135:Large1
|
UTSW |
8 |
73,544,724 (GRCm39) |
missense |
probably benign |
0.38 |
|
R5137:Large1
|
UTSW |
8 |
73,774,937 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R5567:Large1
|
UTSW |
8 |
73,564,081 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R5945:Large1
|
UTSW |
8 |
73,578,828 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6619:Large1
|
UTSW |
8 |
73,609,892 (GRCm39) |
nonsense |
probably null |
|
|
R6951:Large1
|
UTSW |
8 |
73,843,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7041:Large1
|
UTSW |
8 |
73,843,092 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7300:Large1
|
UTSW |
8 |
73,564,224 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7493:Large1
|
UTSW |
8 |
73,550,343 (GRCm39) |
missense |
probably benign |
0.23 |
|
R7877:Large1
|
UTSW |
8 |
73,843,071 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8118:Large1
|
UTSW |
8 |
73,858,572 (GRCm39) |
missense |
probably benign |
0.40 |
|
R8129:Large1
|
UTSW |
8 |
73,542,585 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8525:Large1
|
UTSW |
8 |
73,564,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8963:Large1
|
UTSW |
8 |
73,542,612 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9170:Large1
|
UTSW |
8 |
73,542,645 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9653:Large1
|
UTSW |
8 |
73,564,106 (GRCm39) |
missense |
probably benign |
|
|
Z1088:Large1
|
UTSW |
8 |
73,638,731 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GCTGTTCCATGGGGTAAAGAG -3'
(R):5'- GAAAACTCAAGCCTCTGTGAC -3'
Sequencing Primer
(F):5'- CTGTTCCATGGGGTAAAGAGTATTAG -3'
(R):5'- CACCTCTTGGAGTTAGAGTAAATTG -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation