Incidental Mutation 'R5949:Xylt2'
| ID |
472342 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Xylt2
|
| Ensembl Gene |
ENSMUSG00000020868 |
| Gene Name |
xylosyltransferase II |
| Synonyms |
E030002B02Rik |
| MMRRC Submission |
044139-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.833)
|
| Stock # |
R5949 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
94554677-94568341 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 94559309 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 383
(R383C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112052
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000116349]
[ENSMUST00000146693]
[ENSMUST00000150377]
[ENSMUST00000153485]
|
| AlphaFold |
Q9EPL0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000116349
AA Change: R383C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: R383C
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
13 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
66 |
85 |
N/A |
INTRINSIC |
|
low complexity region
|
102 |
120 |
N/A |
INTRINSIC |
|
Pfam:Branch
|
234 |
489 |
1.9e-60 |
PFAM |
|
Pfam:Xylo_C
|
519 |
699 |
1.2e-71 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000146693
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150377
|
| SMART Domains |
Protein: ENSMUSP00000134495
Gene: ENSMUSG00000020868
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Xylo_C
|
31 |
97 |
2.1e-28 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000153485
AA Change: R383C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: R383C
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
13 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
66 |
85 |
N/A |
INTRINSIC |
|
low complexity region
|
102 |
120 |
N/A |
INTRINSIC |
|
Pfam:Branch
|
234 |
489 |
1.1e-59 |
PFAM |
|
Pfam:Xylo_C
|
519 |
594 |
2.4e-19 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154830
|
| Meta Mutation Damage Score |
0.6954 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 94.1%
|
| Validation Efficiency |
92% (58/63) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an isoform of xylosyltransferase, which belongs to a family of glycosyltransferases. This enzyme transfers xylose from UDP-xylose to specific serine residues of the core protein and initiates the biosynthesis of glycosaminoglycan chains in proteoglycans including chondroitin sulfate, heparan sulfate, heparin and dermatan sulfate. The enzyme activity, which is increased in scleroderma patients, is a diagnostic marker for the determination of sclerotic activity in systemic sclerosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
PHENOTYPE: Mice homozygous for a knock-out allele lack most liver proteoglycans and develop many aspects of polycystic liver and kidney disease, including biliary tract hyperplasia, liver fibrosis, biliary cysts, renal tubule dilation, basement membrane abnormalities and hydronephrosis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2m |
A |
G |
6: 121,655,032 (GRCm39) |
Y1452C |
probably damaging |
Het |
| Adcy10 |
A |
T |
1: 165,367,386 (GRCm39) |
H552L |
possibly damaging |
Het |
| Alms1-ps1 |
A |
T |
6: 85,698,943 (GRCm39) |
|
noncoding transcript |
Het |
| Arhgap21 |
A |
G |
2: 20,853,852 (GRCm39) |
S1837P |
probably damaging |
Het |
| Atad5 |
G |
T |
11: 79,986,835 (GRCm39) |
E641* |
probably null |
Het |
| Atp8b4 |
T |
A |
2: 126,247,242 (GRCm39) |
T276S |
probably benign |
Het |
| Bptf |
A |
G |
11: 107,001,915 (GRCm39) |
I399T |
probably damaging |
Het |
| Carf |
A |
C |
1: 60,178,472 (GRCm39) |
K295T |
probably damaging |
Het |
| Cd209d |
T |
A |
8: 3,927,949 (GRCm39) |
N52Y |
possibly damaging |
Het |
| Cdh2 |
T |
A |
18: 16,734,687 (GRCm39) |
I779F |
probably damaging |
Het |
| Cdon |
G |
A |
9: 35,398,247 (GRCm39) |
R988H |
probably benign |
Het |
| Cfhr4 |
A |
T |
1: 139,660,887 (GRCm39) |
H600Q |
probably damaging |
Het |
| Cic |
C |
T |
7: 24,971,730 (GRCm39) |
T487M |
probably damaging |
Het |
| Dcps |
A |
G |
9: 35,036,557 (GRCm39) |
|
probably benign |
Het |
| Ddx41 |
A |
G |
13: 55,679,874 (GRCm39) |
C427R |
probably damaging |
Het |
| Diras2 |
T |
C |
13: 52,661,747 (GRCm39) |
K187E |
possibly damaging |
Het |
| Emb |
A |
G |
13: 117,403,928 (GRCm39) |
I227V |
probably benign |
Het |
| Fam193a |
T |
A |
5: 34,597,816 (GRCm39) |
S538T |
possibly damaging |
Het |
| Fchsd1 |
C |
T |
18: 38,092,926 (GRCm39) |
|
probably benign |
Het |
| Galnt6 |
A |
T |
15: 100,594,431 (GRCm39) |
N533K |
probably damaging |
Het |
| Grip1 |
A |
G |
10: 119,886,147 (GRCm39) |
D499G |
probably benign |
Het |
| Ifih1 |
T |
C |
2: 62,440,904 (GRCm39) |
N421D |
probably benign |
Het |
| Ifng |
G |
C |
10: 118,278,529 (GRCm39) |
M63I |
probably benign |
Het |
| Ighv1-43 |
A |
G |
12: 114,910,002 (GRCm39) |
M1T |
probably null |
Het |
| Kif20a |
G |
A |
18: 34,765,468 (GRCm39) |
A822T |
probably benign |
Het |
| Krt87 |
A |
T |
15: 101,385,476 (GRCm39) |
C299S |
probably damaging |
Het |
| Lrrn1 |
G |
T |
6: 107,544,465 (GRCm39) |
V88L |
probably benign |
Het |
| Mapkapk2 |
A |
G |
1: 130,985,742 (GRCm39) |
V173A |
possibly damaging |
Het |
| Mrap2 |
T |
G |
9: 87,064,658 (GRCm39) |
V133G |
probably benign |
Het |
| Nlrp1a |
T |
A |
11: 70,989,815 (GRCm39) |
D984V |
probably damaging |
Het |
| Or4c125 |
A |
G |
2: 89,170,229 (GRCm39) |
V139A |
probably damaging |
Het |
| Or5p59 |
T |
C |
7: 107,703,404 (GRCm39) |
L296P |
probably damaging |
Het |
| Pcdh17 |
T |
C |
14: 84,684,996 (GRCm39) |
Y488H |
probably damaging |
Het |
| Pih1d2 |
C |
T |
9: 50,536,284 (GRCm39) |
P313L |
probably damaging |
Het |
| Ralgapb |
T |
C |
2: 158,296,179 (GRCm39) |
C839R |
probably damaging |
Het |
| Rdh5 |
C |
A |
10: 128,754,136 (GRCm39) |
R29L |
probably benign |
Het |
| Rfx6 |
A |
G |
10: 51,554,429 (GRCm39) |
D90G |
probably benign |
Het |
| Rnf213 |
A |
G |
11: 119,333,905 (GRCm39) |
Y3038C |
probably damaging |
Het |
| Sec14l2 |
A |
T |
11: 4,058,972 (GRCm39) |
V191D |
probably damaging |
Het |
| Slc3a2 |
T |
C |
19: 8,690,759 (GRCm39) |
Y118C |
probably damaging |
Het |
| Sorbs2 |
T |
C |
8: 46,222,934 (GRCm39) |
|
probably null |
Het |
| Stab2 |
A |
G |
10: 86,805,713 (GRCm39) |
L211P |
possibly damaging |
Het |
| Tbc1d9b |
T |
C |
11: 50,038,876 (GRCm39) |
C289R |
probably benign |
Het |
| Tfpi |
T |
C |
2: 84,275,092 (GRCm39) |
E172G |
probably benign |
Het |
| Tmem106b |
T |
A |
6: 13,083,418 (GRCm39) |
M229K |
probably damaging |
Het |
| Tsfm |
G |
A |
10: 126,864,244 (GRCm39) |
T157M |
probably damaging |
Het |
| Tshr |
G |
A |
12: 91,503,992 (GRCm39) |
R310H |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,608,244 (GRCm39) |
A17893V |
possibly damaging |
Het |
| Vps39 |
A |
G |
2: 120,159,149 (GRCm39) |
Y380H |
probably benign |
Het |
| Zfp719 |
C |
T |
7: 43,233,541 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Xylt2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02048:Xylt2
|
APN |
11 |
94,557,171 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
IGL02421:Xylt2
|
APN |
11 |
94,558,588 (GRCm39) |
missense |
possibly damaging |
0.45 |
|
P0040:Xylt2
|
UTSW |
11 |
94,559,617 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
PIT4585001:Xylt2
|
UTSW |
11 |
94,557,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0016:Xylt2
|
UTSW |
11 |
94,560,466 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0016:Xylt2
|
UTSW |
11 |
94,560,466 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0313:Xylt2
|
UTSW |
11 |
94,560,720 (GRCm39) |
splice site |
probably benign |
|
|
R0449:Xylt2
|
UTSW |
11 |
94,557,159 (GRCm39) |
missense |
probably benign |
0.22 |
|
R0511:Xylt2
|
UTSW |
11 |
94,560,762 (GRCm39) |
nonsense |
probably null |
|
|
R1483:Xylt2
|
UTSW |
11 |
94,560,393 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1511:Xylt2
|
UTSW |
11 |
94,561,259 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1565:Xylt2
|
UTSW |
11 |
94,558,420 (GRCm39) |
missense |
probably benign |
|
|
R1616:Xylt2
|
UTSW |
11 |
94,559,035 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1702:Xylt2
|
UTSW |
11 |
94,559,571 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1712:Xylt2
|
UTSW |
11 |
94,559,575 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R2233:Xylt2
|
UTSW |
11 |
94,560,822 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R2234:Xylt2
|
UTSW |
11 |
94,560,822 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R4534:Xylt2
|
UTSW |
11 |
94,557,176 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4702:Xylt2
|
UTSW |
11 |
94,560,355 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R4768:Xylt2
|
UTSW |
11 |
94,561,298 (GRCm39) |
missense |
probably benign |
0.06 |
|
R5032:Xylt2
|
UTSW |
11 |
94,560,842 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5237:Xylt2
|
UTSW |
11 |
94,557,953 (GRCm39) |
missense |
probably benign |
|
|
R5281:Xylt2
|
UTSW |
11 |
94,559,616 (GRCm39) |
missense |
probably benign |
0.30 |
|
R6950:Xylt2
|
UTSW |
11 |
94,558,455 (GRCm39) |
missense |
probably benign |
|
|
R7041:Xylt2
|
UTSW |
11 |
94,558,408 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8987:Xylt2
|
UTSW |
11 |
94,561,278 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9029:Xylt2
|
UTSW |
11 |
94,555,462 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9088:Xylt2
|
UTSW |
11 |
94,561,229 (GRCm39) |
missense |
probably benign |
0.32 |
|
R9285:Xylt2
|
UTSW |
11 |
94,558,536 (GRCm39) |
missense |
probably benign |
0.06 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCAGCACTGTGTGGAAGAATG -3'
(R):5'- GGGTTGTAAAGCCCTTAAACC -3'
Sequencing Primer
(F):5'- TGAACCATGGGCTCGTCAAC -3'
(R):5'- CCCTTAAACCAATCATAGGTGAGGG -3'
|
| Posted On |
2017-03-31 |
Incidental Mutation