Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4585001:Xylt2'

556619

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

Accession Numbers

Essential gene?

Probably essential (E-score: 0.872) question?

Stock #

PIT4585001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 94557066 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 745 (V745M)

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: V745M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: V745M

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

SMART Domains

Protein: ENSMUSP00000134495
Gene: ENSMUSG00000020868
AA Change: V142M

Domain	Start	End	E-Value	Type
Pfam:Xylo_C	31	97	2.1e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153485

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868

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

Coding Region Coverage

1x: 93.6%
3x: 91.2%
10x: 86.5%
20x: 76.8%

Validation Efficiency

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aurka	T	C	2: 172,199,117 (GRCm39)	M318V	probably benign	Het
Cacna2d1	T	A	5: 16,531,342 (GRCm39)	D560E	probably damaging	Het
Ccdc148	T	A	2: 58,872,988 (GRCm39)	T202S	probably benign	Het
Cdc42bpb	T	C	12: 111,271,412 (GRCm39)	D1149G	probably damaging	Het
Clasp1	T	A	1: 118,390,285 (GRCm39)	N156K	probably damaging	Het
Cox18	G	A	5: 90,365,434 (GRCm39)	T255I	possibly damaging	Het
Cse1l	A	G	2: 166,783,394 (GRCm39)	T783A	probably damaging	Het
Dnajc16	T	C	4: 141,491,996 (GRCm39)	Y609C	probably damaging	Het
Doc2g	A	G	19: 4,056,630 (GRCm39)	T339A	probably benign	Het
Eif5a	T	C	11: 69,808,896 (GRCm39)		probably benign	Het
Epha3	A	G	16: 63,386,940 (GRCm39)		probably null	Het
Esco1	A	T	18: 10,594,355 (GRCm39)	C310*	probably null	Het
Fam222a	A	G	5: 114,749,101 (GRCm39)	Y99C	probably damaging	Het
Fzd2	T	C	11: 102,496,573 (GRCm39)	L339P	probably damaging	Het
Gfral	A	T	9: 76,104,576 (GRCm39)	N145K	probably damaging	Het
Gga1	T	A	15: 78,777,990 (GRCm39)	N618K	probably benign	Het
Gpatch3	T	A	4: 133,310,397 (GRCm39)	H447Q	probably damaging	Het
Gpn1	A	T	5: 31,666,747 (GRCm39)	R346*	probably null	Het
Gsg1	T	C	6: 135,214,558 (GRCm39)	E317G	probably benign	Het
Gsk3b	A	G	16: 38,004,816 (GRCm39)	N129S	probably damaging	Het
Hmg20b	G	T	10: 81,184,789 (GRCm39)	D94E	possibly damaging	Het
Kash5	C	T	7: 44,849,695 (GRCm39)	G76D	probably benign	Het
Klhdc9	T	A	1: 171,187,386 (GRCm39)	H204L	possibly damaging	Het
Klhl24	A	G	16: 19,925,638 (GRCm39)	I55M	probably benign	Het
Kmt2c	T	C	5: 25,520,104 (GRCm39)	D2002G	probably benign	Het
Lama4	A	G	10: 38,950,742 (GRCm39)	N1015S	probably damaging	Het
Lpp	T	C	16: 24,580,697 (GRCm39)	C263R	probably benign	Het
Lrp1b	T	C	2: 41,159,216 (GRCm39)	I1689V		Het
Mipep	C	A	14: 61,022,284 (GRCm39)	Q50K	probably benign	Het
Mx1	T	C	16: 97,257,454 (GRCm39)	D101G	probably benign	Het
Nabp2	C	G	10: 128,244,676 (GRCm39)	E37Q	possibly damaging	Het
Nme6	A	G	9: 109,671,104 (GRCm39)	I115V	possibly damaging	Het
Nup93	A	T	8: 94,970,355 (GRCm39)	T85S	probably benign	Het
Oit3	T	A	10: 59,266,835 (GRCm39)	I224F	possibly damaging	Het
Parp14	T	C	16: 35,678,975 (GRCm39)	K331R	probably benign	Het
Pls1	T	A	9: 95,643,443 (GRCm39)	T519S	probably benign	Het
Rcn3	A	G	7: 44,736,118 (GRCm39)	F197L	probably benign	Het
Rnf213	C	T	11: 119,349,218 (GRCm39)	T3773I		Het
Rprd1b	A	T	2: 157,889,877 (GRCm39)	I153L	probably benign	Het
Scel	A	G	14: 103,829,804 (GRCm39)	D462G	possibly damaging	Het
Sh3bp1	C	T	15: 78,794,276 (GRCm39)	S548L	possibly damaging	Het
Sim1	T	A	10: 50,860,284 (GRCm39)	Y715*	probably null	Het
Slc18a2	A	T	19: 59,282,293 (GRCm39)	Q500L	possibly damaging	Het
Slc5a8	T	G	10: 88,722,365 (GRCm39)	M66R	probably damaging	Het
Slco1a6	T	C	6: 142,055,246 (GRCm39)	T233A	probably damaging	Het
Smu1	T	C	4: 40,739,623 (GRCm39)	T396A	probably benign	Het
Tas2r104	T	C	6: 131,662,521 (GRCm39)	T63A	possibly damaging	Het
Tasor2	G	A	13: 3,624,979 (GRCm39)	A1657V	possibly damaging	Het
Top2a	C	T	11: 98,892,199 (GRCm39)	A1088T	probably benign	Het
Ucp1	T	C	8: 84,020,577 (GRCm39)	F129S	probably damaging	Het
Unc13b	T	A	4: 43,091,298 (GRCm39)	D41E	probably benign	Het
Usp10	T	G	8: 120,681,631 (GRCm39)	V696G	probably benign	Het
Zbtb49	A	T	5: 38,373,820 (GRCm39)	N41K	probably damaging	Het
Zfp109	T	A	7: 23,928,779 (GRCm39)	D218V	probably benign	Het
Zfp420	G	A	7: 29,575,430 (GRCm39)	R550Q	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
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
R5949:Xylt2	UTSW	11	94,559,309 (GRCm39)	missense	probably damaging	1.00
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'- GGCTGAGTTATAATGGCAGAGC -3'
(R):5'- ACGTCTCTTCCGGAACTTTGG -3'

Sequencing Primer
(F):5'- GAGCCACATTTCAAACTAGTCTG -3'
(R):5'- ACCACTGGATGAGCCCGTAG -3'

Posted On

2019-06-07