Mutagenetix > Incidental Mutations

Incidental Mutation 'R1616:Xylt2'

174281

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

039653-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.587) question?

Stock #

R1616 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

94663851-94677515 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 94668209 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 445 (S445N)

Ref Sequence

ENSEMBL: ENSMUSP00000112052 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000116349
AA Change: S445N

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: S445N

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: S445N

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: S445N

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: 98.8%
3x: 97.8%
10x: 94.3%
20x: 85.3%

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933406P04Rik	T	C	10: 20,311,341		probably benign	Het
A1cf	A	G	19: 31,934,775	E430G	probably damaging	Het
Aacs	T	A	5: 125,484,526		probably null	Het
Acot12	G	A	13: 91,772,767	V331I	probably benign	Het
Acp7	A	G	7: 28,611,078	W445R	probably damaging	Het
Actl11	C	A	9: 107,931,936	Q1153K	probably benign	Het
Actr8	A	G	14: 29,982,644	T34A	possibly damaging	Het
Ahnak	A	G	19: 9,008,987	D2545G	possibly damaging	Het
Ap5z1	A	G	5: 142,472,236	Y388C	probably benign	Het
Apol7a	C	T	15: 77,389,606	G219S	probably damaging	Het
Arid1b	T	A	17: 5,339,294	I1705N	probably damaging	Het
Bod1l	T	C	5: 41,808,715	Q2669R	probably benign	Het
Braf	A	T	6: 39,643,133	S504T	probably benign	Het
Cbl	A	T	9: 44,152,900	Y780N	probably damaging	Het
Cd86	T	C	16: 36,628,976	I20V	probably benign	Het
Cep290	T	G	10: 100,568,836	D2353E	probably benign	Het
Ckmt2	G	A	13: 91,859,209	R289C	probably benign	Het
Col3a1	T	C	1: 45,328,488		probably null	Het
Cyp4f16	T	A	17: 32,542,968	Y163*	probably null	Het
Dimt1	T	C	13: 106,953,450	V227A	possibly damaging	Het
Dnah6	A	T	6: 73,100,112	M2338K	probably benign	Het
Dock4	T	G	12: 40,669,045	I274S	probably damaging	Het
Enthd1	T	C	15: 80,452,385	D616G	probably damaging	Het
Fignl2	T	C	15: 101,054,116	E95G	probably damaging	Het
Foxn1	A	G	11: 78,358,866	M611T	probably benign	Het
Foxs1	T	C	2: 152,932,639	S165G	probably benign	Het
Fzd3	G	T	14: 65,235,507	Q271K	probably benign	Het
Hadhb	A	T	5: 30,166,715	I55F	probably damaging	Het
Hipk3	G	A	2: 104,433,745	Q824*	probably null	Het
Hps1	G	A	19: 42,767,185	R201W	probably damaging	Het
Kif21b	T	C	1: 136,171,685	S1477P	probably damaging	Het
Kif26a	A	T	12: 112,157,246		probably null	Het
Krt90	T	C	15: 101,560,591	E172G	possibly damaging	Het
Lama4	T	G	10: 39,075,450	F1064V	probably damaging	Het
Leng9	A	G	7: 4,148,903	V258A	probably benign	Het
Lgi2	A	C	5: 52,546,638	V217G	probably benign	Het
Lpgat1	T	C	1: 191,763,629	I310T	possibly damaging	Het
Ltbp3	A	G	19: 5,746,967	Y374C	probably damaging	Het
Magi2	C	A	5: 20,609,326	T1075K	probably damaging	Het
Man2c1	T	C	9: 57,135,509	I221T	probably benign	Het
Mydgf	A	G	17: 56,179,415	M72T	possibly damaging	Het
Myo1b	T	C	1: 51,776,315	N624S	probably damaging	Het
Myo5c	T	A	9: 75,296,017	M1465K	probably damaging	Het
Nek4	A	T	14: 30,987,137	D716V	probably damaging	Het
Nfxl1	T	A	5: 72,529,037	Q607L	probably benign	Het
Nlrp9c	A	T	7: 26,384,437	D572E	probably benign	Het
Nop14	G	T	5: 34,650,413	Q402K	possibly damaging	Het
Npy5r	C	G	8: 66,681,400	C247S	probably damaging	Het
Nrap	T	A	19: 56,389,823	I19F	probably damaging	Het
Olfr1189	A	G	2: 88,592,008	D68G	probably damaging	Het
Olfr1336	T	G	7: 6,460,745	S79A	probably damaging	Het
Olfr574	T	A	7: 102,948,514	N16K	probably damaging	Het
Pcdh9	A	T	14: 93,886,969	Y588*	probably null	Het
Ppp1r12a	A	G	10: 108,260,867	E183G	probably damaging	Het
Ppp2r2b	T	A	18: 42,688,310	H261L	probably benign	Het
Ptch1	G	T	13: 63,539,842	T374K	possibly damaging	Het
Ptpn13	A	T	5: 103,565,237	N1742I	possibly damaging	Het
Rab33a	C	T	X: 48,519,644	S15L	probably benign	Het
Ralb	T	C	1: 119,478,014	Y75C	probably damaging	Het
Rassf7	T	A	7: 141,216,732	V2D	probably damaging	Het
Rbm10	A	G	X: 20,645,991	N397S	probably benign	Het
Rbm15	T	C	3: 107,330,881	T734A	probably benign	Het
Rbm8a	G	T	3: 96,631,730		probably benign	Het
Rock2	T	C	12: 16,972,985	I1095T	probably benign	Het
Rxfp3	T	A	15: 11,036,303	T328S	probably damaging	Het
Sec31a	T	A	5: 100,386,195	K505N	possibly damaging	Het
Selenof	A	G	3: 144,596,881	*122W	probably null	Het
Sh3pxd2b	T	C	11: 32,381,441	M55T	possibly damaging	Het
Slc15a2	T	C	16: 36,754,481	D522G	probably benign	Het
Slc2a1	T	C	4: 119,136,306	F447L	probably damaging	Het
Slc45a2	T	A	15: 11,022,128	C319S	probably null	Het
Smad4	T	C	18: 73,640,262	D551G	probably benign	Het
Smarcc2	A	G	10: 128,482,793	Y648C	probably damaging	Het
Snrnp40	C	G	4: 130,378,043		probably null	Het
Stab2	A	T	10: 86,885,718		probably null	Het
Tanc1	A	G	2: 59,785,387	D246G	probably damaging	Het
Tekt3	T	G	11: 63,087,198		probably null	Het
Them5	G	A	3: 94,346,260		probably null	Het
Tlr4	T	A	4: 66,839,480	F170Y	probably damaging	Het
Tmem214	T	G	5: 30,871,563	Y165*	probably null	Het
Tmem94	T	C	11: 115,796,145		probably null	Het
Tom1l1	A	G	11: 90,656,351	L301S	possibly damaging	Het
Trpm3	A	G	19: 22,982,712	E1237G	probably damaging	Het
Ube2d1	C	A	10: 71,256,693	C107F	probably damaging	Het
Ugt3a1	C	T	15: 9,306,244	R160*	probably null	Het
Vcan	G	A	13: 89,705,663	P393S	probably damaging	Het
Virma	T	C	4: 11,544,954	F1638L	probably damaging	Het
Vmn1r31	G	A	6: 58,472,058	T274I	probably damaging	Het
Zfp457	A	G	13: 67,296,311	F43L	possibly damaging	Het
Zfp879	T	A	11: 50,832,646	M455L	probably benign	Het

Other mutations in Xylt2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02048:Xylt2	APN	11	94666345	missense	possibly damaging	0.61
IGL02421:Xylt2	APN	11	94667762	missense	possibly damaging	0.45
P0040:Xylt2	UTSW	11	94668791	missense	possibly damaging	0.46
R0016:Xylt2	UTSW	11	94669640	missense	probably damaging	1.00
R0016:Xylt2	UTSW	11	94669640	missense	probably damaging	1.00
R0313:Xylt2	UTSW	11	94669894	splice site	probably benign
R0449:Xylt2	UTSW	11	94666333	missense	probably benign	0.22
R0511:Xylt2	UTSW	11	94669936	nonsense	probably null
R1483:Xylt2	UTSW	11	94669567	missense	probably benign	0.04
R1511:Xylt2	UTSW	11	94670433	missense	probably damaging	1.00
R1565:Xylt2	UTSW	11	94667594	missense	probably benign
R1702:Xylt2	UTSW	11	94668745	missense	probably damaging	0.98
R1712:Xylt2	UTSW	11	94668749	missense	possibly damaging	0.88
R2233:Xylt2	UTSW	11	94669996	missense	possibly damaging	0.71
R2234:Xylt2	UTSW	11	94669996	missense	possibly damaging	0.71
R4534:Xylt2	UTSW	11	94666350	missense	probably benign	0.02
R4702:Xylt2	UTSW	11	94669529	missense	possibly damaging	0.83
R4768:Xylt2	UTSW	11	94670472	missense	probably benign	0.06
R5032:Xylt2	UTSW	11	94670016	missense	probably damaging	0.99
R5237:Xylt2	UTSW	11	94667127	missense	probably benign
R5281:Xylt2	UTSW	11	94668790	missense	probably benign	0.30
R5949:Xylt2	UTSW	11	94668483	missense	probably damaging	1.00
R6950:Xylt2	UTSW	11	94667629	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GCCTCTCTGACCCTGAAAGTTTACG -3'
(R):5'- ATGCTGGTTGCCAGGTGGAAAG -3'

Sequencing Primer
(F):5'- CCTGAAAGTTTACGGGGGAAC -3'
(R):5'- ACACGCAGCTTTGTGGAATATG -3'

Posted On

2014-04-24