Mutagenetix > Incidental Mutation

Incidental Mutation 'R5032:Xylt2'

391772

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

042623-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.872) question?

Stock #

R5032 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 94560842 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 232 (V232E)

Ref Sequence

ENSEMBL: ENSMUSP00000122581 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000116349] [ENSMUST00000146693] [ENSMUST00000150377] [ENSMUST00000153485]

AlphaFold

Q9EPL0

Predicted Effect

probably damaging
Transcript: ENSMUST00000116349
AA Change: V232E

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: V232E

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: V232E

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: V232E

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

0.9464

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.6%
20x: 93.0%

Validation Efficiency

97% (77/79)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700012B07Rik	G	T	11: 109,684,980 (GRCm39)	C172*	probably null	Het
Actl9	A	G	17: 33,653,062 (GRCm39)	N374S	probably benign	Het
Adam34l	T	C	8: 44,079,508 (GRCm39)	N239D	probably damaging	Het
Ahcyl2	T	A	6: 29,768,555 (GRCm39)		probably benign	Het
Arfgef2	T	C	2: 166,720,464 (GRCm39)	M1501T	probably benign	Het
Asb17	A	T	3: 153,550,175 (GRCm39)	D69V	probably damaging	Het
Atp13a5	T	C	16: 29,082,202 (GRCm39)	Y877C	probably damaging	Het
Atrip	T	C	9: 108,894,271 (GRCm39)	Q64R	probably benign	Het
Auts2	A	G	5: 131,505,730 (GRCm39)		probably benign	Het
Cacna2d1	G	T	5: 16,564,068 (GRCm39)	R893L	probably damaging	Het
Ccdc138	C	T	10: 58,409,458 (GRCm39)	R596C	probably damaging	Het
Cd163	A	G	6: 124,288,628 (GRCm39)	Y353C	probably damaging	Het
Cdon	T	C	9: 35,400,330 (GRCm39)	Y1015H	probably damaging	Het
Chsy3	T	C	18: 59,312,543 (GRCm39)	Y339H	probably damaging	Het
Cspp1	T	C	1: 10,136,744 (GRCm39)	W190R	probably benign	Het
Ddx1	A	T	12: 13,273,993 (GRCm39)	I570N	probably damaging	Het
Duox1	G	A	2: 122,167,798 (GRCm39)	R1027H	probably benign	Het
Dync1h1	C	T	12: 110,593,326 (GRCm39)	Q1198*	probably null	Het
Ecel1	G	A	1: 87,081,975 (GRCm39)	S246L	probably damaging	Het
Fam228b	T	G	12: 4,813,042 (GRCm39)	R109S	probably damaging	Het
Fut9	T	A	4: 25,799,245 (GRCm39)		probably benign	Het
Gm5592	A	G	7: 40,939,159 (GRCm39)	R814G	probably damaging	Het
Gmps	A	G	3: 63,897,746 (GRCm39)	K233E	probably benign	Het
Gramd1c	A	G	16: 43,811,026 (GRCm39)	Y438H	probably damaging	Het
Gsdmc	A	T	15: 63,673,882 (GRCm39)	D134E	possibly damaging	Het
Gxylt2	A	G	6: 100,760,142 (GRCm39)	I226V	probably benign	Het
Hc	T	C	2: 34,903,544 (GRCm39)	I1037V	probably benign	Het
Hspa4	T	G	11: 53,179,950 (GRCm39)	R69S	possibly damaging	Het
Hspg2	C	T	4: 137,246,251 (GRCm39)	R1010C	probably damaging	Het
Kifc3	A	G	8: 95,829,354 (GRCm39)	S508P	probably damaging	Het
Krt7	G	A	15: 101,310,428 (GRCm39)	R25H	probably benign	Het
Lhfpl6	T	A	3: 52,950,854 (GRCm39)	S43T	possibly damaging	Het
Lrrc7	T	A	3: 157,887,217 (GRCm39)	K394N	possibly damaging	Het
Lypd4	A	T	7: 24,566,240 (GRCm39)	L28Q	probably damaging	Het
Mdc1	A	G	17: 36,161,481 (GRCm39)	E798G	probably benign	Het
Mta1	T	A	12: 113,097,145 (GRCm39)		probably null	Het
Mtg2	A	T	2: 179,725,183 (GRCm39)	Q132L	possibly damaging	Het
Myh1	G	T	11: 67,096,874 (GRCm39)	E382*	probably null	Het
Myo3a	T	C	2: 22,287,413 (GRCm39)	L175P	probably damaging	Het
Nckap5	A	T	1: 125,904,786 (GRCm39)	F144L	possibly damaging	Het
Nfrkb	T	A	9: 31,300,351 (GRCm39)		probably null	Het
Nmt2	C	T	2: 3,285,429 (GRCm39)	P5L	probably benign	Het
Nsmf	T	C	2: 24,945,073 (GRCm39)		probably null	Het
Oprl1	C	T	2: 181,360,795 (GRCm39)	R257C	probably damaging	Het
Or51q1	A	T	7: 103,628,581 (GRCm39)	M61L	probably damaging	Het
Or5a1	T	A	19: 12,097,420 (GRCm39)	I219F	probably benign	Het
Pcdhgc3	T	A	18: 37,940,638 (GRCm39)	N346K	probably damaging	Het
Pcnt	G	A	10: 76,190,911 (GRCm39)	P2791S	probably benign	Het
Pdia3	A	G	2: 121,244,620 (GRCm39)	N11S	probably benign	Het
Pik3c2g	A	T	6: 139,841,928 (GRCm39)	T778S	probably benign	Het
Pik3ip1	T	A	11: 3,283,520 (GRCm39)	I75N	probably damaging	Het
Pla2g4d	A	T	2: 120,112,176 (GRCm39)	Y118*	probably null	Het
Ppargc1b	A	G	18: 61,440,336 (GRCm39)	S845P	probably damaging	Het
Prdm2	A	T	4: 142,905,937 (GRCm39)	L50*	probably null	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Pxdn	G	A	12: 30,053,140 (GRCm39)	V926I	probably benign	Het
Rab11fip2	A	T	19: 59,925,799 (GRCm39)	N139K	probably damaging	Het
Rcn2	T	A	9: 55,960,300 (GRCm39)	M189K	probably damaging	Het
Rev1	A	T	1: 38,113,570 (GRCm39)		probably benign	Het
Rhbg	C	A	3: 88,152,441 (GRCm39)	G368C	probably damaging	Het
Rnf214	A	G	9: 45,811,042 (GRCm39)		probably null	Het
Sf3a3	T	C	4: 124,618,959 (GRCm39)	S307P	probably benign	Het
Slc6a18	T	A	13: 73,814,442 (GRCm39)	Y494F	probably damaging	Het
Son	T	C	16: 91,454,552 (GRCm39)	S1100P	probably damaging	Het
Spag16	T	G	1: 69,892,511 (GRCm39)	N97K	probably benign	Het
Tmem192	T	C	8: 65,412,163 (GRCm39)	V114A	possibly damaging	Het
Urb1	G	T	16: 90,553,059 (GRCm39)	P1901T	probably benign	Het
Vwa5b2	A	G	16: 20,419,459 (GRCm39)	T601A	probably damaging	Het
Wdtc1	G	T	4: 133,036,162 (GRCm39)	T126K	possibly damaging	Het
Xirp2	T	C	2: 67,356,014 (GRCm39)	Y3592H	possibly damaging	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
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'- ACAACCTTTAGAGTCTCTGCTC -3'
(R):5'- GGCCCAGATCTTCATGCTTC -3'

Sequencing Primer
(F):5'- CTGTTCAGCCAGAGCCTCTG -3'
(R):5'- GCTATATGTACCGATTGGCAGAG -3'

Posted On

2016-06-06