Mutagenetix > Incidental Mutation

Incidental Mutation 'R2234:Xylt2'

239942

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

040235-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.872) question?

Stock #

R2234 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 94560822 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 239 (V239M)

Ref Sequence

ENSEMBL: ENSMUSP00000122581 (fasta)

Gene Model

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

AlphaFold

Q9EPL0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000116349
AA Change: V239M

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: V239M

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

possibly damaging
Transcript: ENSMUST00000153485
AA Change: V239M

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: V239M

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

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.1%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acbd6	A	G	1: 155,434,454 (GRCm39)	D24G	probably damaging	Het
Adarb1	A	G	10: 77,153,183 (GRCm39)	V322A	probably damaging	Het
Akap8l	C	T	17: 32,557,777 (GRCm39)	G37R	probably damaging	Het
BC035947	A	T	1: 78,474,599 (GRCm39)	D644E	probably damaging	Het
Capzb	T	A	4: 138,989,334 (GRCm39)	D85E	possibly damaging	Het
Cd81	T	A	7: 142,620,056 (GRCm39)	N71K	probably benign	Het
Cemip	G	T	7: 83,647,770 (GRCm39)	D103E	probably benign	Het
Chfr	A	G	5: 110,318,729 (GRCm39)	K580E	probably damaging	Het
Chrnb1	A	T	11: 69,686,428 (GRCm39)	I64N	probably damaging	Het
Clca3a1	G	T	3: 144,714,829 (GRCm39)	P596Q	possibly damaging	Het
Cpb1	A	T	3: 20,329,629 (GRCm39)	D32E	probably benign	Het
Crh	A	T	3: 19,748,096 (GRCm39)	M182K	probably damaging	Het
Csta1	C	T	16: 35,945,445 (GRCm39)	V23I	probably damaging	Het
Dazap1	A	G	10: 80,113,433 (GRCm39)	K110E	possibly damaging	Het
Dhx16	T	C	17: 36,198,778 (GRCm39)	C737R	probably damaging	Het
Dync1i2	C	T	2: 71,079,764 (GRCm39)	Q419*	probably null	Het
Eml5	A	C	12: 98,807,840 (GRCm39)	D984E	probably damaging	Het
Fat3	G	A	9: 15,909,567 (GRCm39)	S2145F	probably damaging	Het
Gm12695	C	T	4: 96,612,266 (GRCm39)	R499Q	probably damaging	Het
Hid1	A	G	11: 115,241,945 (GRCm39)	I555T	probably damaging	Het
Hspa2	A	G	12: 76,451,419 (GRCm39)	T38A	possibly damaging	Het
Igf1r	T	A	7: 67,861,828 (GRCm39)	N1129K	probably damaging	Het
Iglon5	T	C	7: 43,130,062 (GRCm39)	E34G	probably damaging	Het
Itprid1	A	T	6: 55,874,797 (GRCm39)	H249L	possibly damaging	Het
Kalrn	C	A	16: 33,996,632 (GRCm39)		probably null	Het
Kmt2d	T	C	15: 98,763,129 (GRCm39)	D240G	probably damaging	Het
Lrrc56	T	A	7: 140,778,207 (GRCm39)	D66E	probably damaging	Het
Myot	A	G	18: 44,487,339 (GRCm39)	D392G	probably damaging	Het
Nphp3	G	A	9: 103,914,575 (GRCm39)	R1052H	probably benign	Het
Obscn	T	C	11: 59,022,472 (GRCm39)	R758G	possibly damaging	Het
Or2d4	C	A	7: 106,543,827 (GRCm39)	C127F	probably damaging	Het
Or4c114	A	G	2: 88,904,592 (GRCm39)	L281P	probably damaging	Het
Or6z5	T	C	7: 6,477,441 (GRCm39)	S111P	possibly damaging	Het
Or7g19	A	T	9: 18,856,112 (GRCm39)	H56L	probably damaging	Het
Or8k39	A	G	2: 86,563,921 (GRCm39)	F12L	possibly damaging	Het
Pax8	A	G	2: 24,333,114 (GRCm39)	I77T	probably damaging	Het
Paxbp1	T	C	16: 90,831,822 (GRCm39)	I355M	probably benign	Het
Pds5a	A	T	5: 65,811,441 (GRCm39)	F331I	probably damaging	Het
Plec	A	T	15: 76,061,147 (GRCm39)	I2952N	probably damaging	Het
Ppp1r12a	A	G	10: 108,034,780 (GRCm39)	I108M	possibly damaging	Het
Rabepk	A	T	2: 34,685,246 (GRCm39)	I58N	possibly damaging	Het
Rnf216	G	A	5: 143,076,681 (GRCm39)	H68Y	probably benign	Het
Scap	T	C	9: 110,210,661 (GRCm39)	C998R	probably damaging	Het
Scgb1b27	T	C	7: 33,721,249 (GRCm39)	Y46H	probably damaging	Het
Sf3a2	G	T	10: 80,638,663 (GRCm39)	A95S	probably benign	Het
Smg7	A	T	1: 152,744,064 (GRCm39)	Y40N	probably damaging	Het
Ssc5d	A	G	7: 4,946,849 (GRCm39)	T1068A	probably benign	Het
Stambp	A	G	6: 83,528,960 (GRCm39)	S362P	probably damaging	Het
Tbx18	G	T	9: 87,606,403 (GRCm39)	S247R	probably damaging	Het
Tenm3	T	C	8: 48,729,204 (GRCm39)	I1601V	probably benign	Het
Thap4	G	T	1: 93,652,934 (GRCm39)	Q441K	probably benign	Het
Tmprss11c	G	T	5: 86,429,945 (GRCm39)	T40K	probably benign	Het
Tnk1	C	T	11: 69,746,017 (GRCm39)		probably null	Het
Trim65	G	T	11: 116,021,503 (GRCm39)	T110K	possibly damaging	Het
Uck1	T	C	2: 32,148,315 (GRCm39)	D167G	probably damaging	Het
Vmn2r124	A	T	17: 18,269,927 (GRCm39)	H61L	possibly damaging	Het
Xpnpep1	T	G	19: 53,001,892 (GRCm39)	D118A	probably 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
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'- ACCTTATGCTTGACCATGCTG -3'
(R):5'- TAGGGCTCTGAGTCTAGGCTTC -3'

Sequencing Primer
(F):5'- GCTCTTGGTATCTAGCCAACAAC -3'
(R):5'- CTTCTGTTAGGAGGCAAGCAG -3'

Posted On

2014-10-15