Mutagenetix > Incidental Mutation

Incidental Mutation 'R1702:Xylt2'

189819

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

039735-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.872) question?

Stock #

R1702 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 94559571 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 357 (H357L)

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: H357L

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: H357L

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: H357L

PolyPhen 2 Score 0.939 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: H357L

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: 98.6%
10x: 96.9%
20x: 94.5%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	T	C	7: 119,981,925 (GRCm39)	V1080A	probably benign	Het
Abcg4	A	C	9: 44,186,370 (GRCm39)	V553G	probably damaging	Het
Ache	T	C	5: 137,289,251 (GRCm39)	V319A	possibly damaging	Het
Acsm2	T	A	7: 119,172,787 (GRCm39)	M134K	possibly damaging	Het
Ank2	A	T	3: 126,749,548 (GRCm39)	S494T	probably benign	Het
Asic3	A	T	5: 24,620,454 (GRCm39)	T202S	probably damaging	Het
Baiap3	T	A	17: 25,463,779 (GRCm39)	H886L	probably damaging	Het
Bltp2	T	A	11: 78,179,854 (GRCm39)	C2126S	probably damaging	Het
Cidea	T	A	18: 67,499,491 (GRCm39)	I126K	probably damaging	Het
Cmklr1	T	G	5: 113,751,903 (GRCm39)	K366T	probably benign	Het
Cntrl	A	T	2: 35,061,848 (GRCm39)		probably null	Het
Crhr2	A	G	6: 55,069,520 (GRCm39)	F378S	probably damaging	Het
Deaf1	C	G	7: 140,894,867 (GRCm39)	R303T	probably damaging	Het
Dnah9	T	A	11: 65,976,021 (GRCm39)	N1343Y	possibly damaging	Het
Dop1b	A	G	16: 93,544,509 (GRCm39)	K99E	possibly damaging	Het
Dpp4	A	T	2: 62,216,773 (GRCm39)		probably null	Het
Dst	T	C	1: 34,206,421 (GRCm39)	V598A	probably damaging	Het
Ece2	C	T	16: 20,449,996 (GRCm39)	R136C	probably damaging	Het
Efcab3	C	T	11: 104,581,832 (GRCm39)	P58L	probably benign	Het
Egf	C	A	3: 129,484,460 (GRCm39)	V453L	probably benign	Het
Egr3	T	A	14: 70,317,216 (GRCm39)	F342L	probably damaging	Het
Eif2ak2	A	T	17: 79,164,063 (GRCm39)	I434N	probably damaging	Het
Emc1	A	G	4: 139,102,512 (GRCm39)	T936A	probably damaging	Het
Fmod	A	T	1: 133,968,500 (GRCm39)	E180V	probably damaging	Het
Gabrg3	T	C	7: 56,634,848 (GRCm39)	T112A	probably damaging	Het
Gak	T	C	5: 108,754,242 (GRCm39)		probably null	Het
Gas2	T	A	7: 51,603,089 (GRCm39)		probably null	Het
Gm2381	T	A	7: 42,469,655 (GRCm39)	Q156H	probably benign	Het
Golga2	T	A	2: 32,189,287 (GRCm39)	S273T	probably damaging	Het
Homez	T	A	14: 55,094,452 (GRCm39)	T419S	probably damaging	Het
Igfbp6	T	A	15: 102,056,617 (GRCm39)	Y184*	probably null	Het
Il11	A	G	7: 4,776,733 (GRCm39)	S86P	probably damaging	Het
Itgal	A	G	7: 126,904,197 (GRCm39)	N270S	probably benign	Het
Lama2	T	C	10: 27,066,525 (GRCm39)	R1119G	probably benign	Het
Lamp3	G	T	16: 19,494,822 (GRCm39)	N294K	probably benign	Het
Mars1	T	C	10: 127,145,948 (GRCm39)	I113M	possibly damaging	Het
Mgat5b	A	G	11: 116,839,485 (GRCm39)	T334A	possibly damaging	Het
Mis18bp1	A	G	12: 65,208,518 (GRCm39)	I65T	probably benign	Het
Mmrn2	A	T	14: 34,119,871 (GRCm39)	N247I	probably benign	Het
Muc6	G	T	7: 141,236,752 (GRCm39)	N322K	probably damaging	Het
Mx2	A	G	16: 97,359,883 (GRCm39)	H551R	probably benign	Het
Mylk	T	A	16: 34,742,314 (GRCm39)	V942E	probably benign	Het
Nes	A	G	3: 87,883,286 (GRCm39)	E515G	probably benign	Het
Nfatc3	T	G	8: 106,818,792 (GRCm39)	S503R	probably damaging	Het
Nkain3	C	A	4: 20,158,339 (GRCm39)		probably null	Het
Noxa1	A	G	2: 24,982,596 (GRCm39)	V73A	probably damaging	Het
Nup160	A	T	2: 90,514,302 (GRCm39)	E83D	probably damaging	Het
Or12j3	A	T	7: 139,952,655 (GRCm39)	Y289*	probably null	Het
Or4z4	C	A	19: 12,076,530 (GRCm39)	V158L	probably benign	Het
Or5ac23	C	A	16: 59,149,504 (GRCm39)	V123L	probably benign	Het
Or8b56	A	G	9: 38,739,839 (GRCm39)	Y284C	probably damaging	Het
Plxnb2	A	G	15: 89,046,187 (GRCm39)		probably null	Het
Rundc3b	A	G	5: 8,562,318 (GRCm39)	V350A	probably benign	Het
Scn1a	C	T	2: 66,148,567 (GRCm39)	D993N	probably damaging	Het
Sec24c	G	T	14: 20,736,641 (GRCm39)	G226V	probably null	Het
Septin11	T	A	5: 93,304,783 (GRCm39)	I200N	probably damaging	Het
Shank3	G	T	15: 89,384,099 (GRCm39)	G14C	probably damaging	Het
Skic3	A	G	13: 76,270,862 (GRCm39)	K153R	possibly damaging	Het
Slc25a39	T	C	11: 102,297,452 (GRCm39)	D5G	possibly damaging	Het
Stoml3	A	T	3: 53,412,852 (GRCm39)	T169S	probably benign	Het
Taf1b	T	A	12: 24,559,125 (GRCm39)	I83K	possibly damaging	Het
Tarbp1	T	A	8: 127,154,957 (GRCm39)	Q1389L	probably damaging	Het
Thbs1	T	A	2: 117,943,923 (GRCm39)	D180E	probably benign	Het
Tmc5	T	A	7: 118,271,462 (GRCm39)	V925D	probably benign	Het
Tmem62	T	C	2: 120,809,708 (GRCm39)	V130A	probably damaging	Het
Tpp2	C	T	1: 44,029,708 (GRCm39)	P997L	probably damaging	Het
Trip12	A	T	1: 84,722,784 (GRCm39)	I127N	probably damaging	Het
Upp2	T	C	2: 58,661,562 (GRCm39)	F142L	possibly damaging	Het
Usf3	C	T	16: 44,039,995 (GRCm39)	Q1492*	probably null	Het
Vcp	T	C	4: 42,990,840 (GRCm39)	D205G	probably damaging	Het
Vmn1r180	G	A	7: 23,652,394 (GRCm39)	V186I	possibly damaging	Het
Washc2	T	C	6: 116,206,267 (GRCm39)	S496P	probably damaging	Het
Wee2	T	C	6: 40,441,135 (GRCm39)	I480T	probably benign	Het
Zbed4	T	C	15: 88,665,056 (GRCm39)	S375P	probably damaging	Het
Zfp442	A	T	2: 150,251,100 (GRCm39)	Y266*	probably null	Het
Zfp600	A	G	4: 146,133,497 (GRCm39)	T722A	probably benign	Het
Zfp976	T	A	7: 42,265,424 (GRCm39)	H55L	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
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'- TGACCAAAGGTCCCACAAAATGGAG -3'
(R):5'- GGCTGGTAAAAGGTGGTCTGATGAC -3'

Sequencing Primer
(F):5'- AATGGAGCCCAGCCTTCTTTC -3'
(R):5'- caccctcacacagacagac -3'

Posted On

2014-05-14