Mutagenetix > Incidental Mutation

Incidental Mutation 'R1565:Xylt2'

175213

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

039604-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.833) question?

Stock #

R1565 (G1)

Quality Score

146

Status

Validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 94558420 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 579 (A579T)

Ref Sequence

ENSEMBL: ENSMUSP00000122581 (fasta)

Gene Model

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

AlphaFold

Q9EPL0

Predicted Effect

probably benign
Transcript: ENSMUST00000116349
AA Change: A579T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: A579T

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 benign
Transcript: ENSMUST00000153485
AA Change: A579T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: A579T

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

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.5%
20x: 90.0%

Validation Efficiency

96% (82/85)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810021J22Rik	G	A	11: 58,771,327 (GRCm39)	G270S	probably benign	Het
Abtb1	T	C	6: 88,813,536 (GRCm39)	T401A	probably benign	Het
Adamts14	A	T	10: 61,106,676 (GRCm39)	M148K	probably damaging	Het
Adcy5	A	G	16: 35,089,327 (GRCm39)	E508G	probably damaging	Het
Ankfy1	T	A	11: 72,648,144 (GRCm39)	L875H	probably damaging	Het
Cacng3	A	T	7: 122,367,624 (GRCm39)	D168V	probably damaging	Het
Clpb	G	A	7: 101,434,668 (GRCm39)	R488Q	probably benign	Het
Cltrn	A	G	X: 162,901,230 (GRCm39)	D184G	possibly damaging	Het
Cpxm2	A	T	7: 131,663,874 (GRCm39)	Y350N	probably damaging	Het
D130040H23Rik	T	A	8: 69,755,812 (GRCm39)	*406R	probably null	Het
Dnah10	T	A	5: 124,906,678 (GRCm39)	D4236E	probably damaging	Het
Dpf3	T	A	12: 83,417,391 (GRCm39)	Y27F	probably damaging	Het
Esp4	T	C	17: 40,913,486 (GRCm39)	*118Q	probably null	Het
Fam222b	T	C	11: 78,045,488 (GRCm39)	S222P	possibly damaging	Het
Flnc	T	C	6: 29,455,170 (GRCm39)	V1933A	probably damaging	Het
Gem	T	C	4: 11,713,709 (GRCm39)	F282L	possibly damaging	Het
Gli2	T	C	1: 118,769,660 (GRCm39)	T631A	possibly damaging	Het
Gpld1	T	A	13: 25,140,051 (GRCm39)	V116E	probably damaging	Het
Gpr176	A	G	2: 118,110,695 (GRCm39)	M188T	probably benign	Het
Grk5	T	C	19: 61,078,410 (GRCm39)	V489A	probably damaging	Het
Hpdl	T	C	4: 116,678,080 (GRCm39)	N127S	probably damaging	Het
Hsd17b8	C	T	17: 34,246,469 (GRCm39)	V105I	possibly damaging	Het
Id4	G	T	13: 48,415,770 (GRCm39)	V151L	possibly damaging	Het
Kcnh8	G	T	17: 53,263,909 (GRCm39)	G802V	probably benign	Het
Lamc1	C	A	1: 153,118,489 (GRCm39)	S894I	probably benign	Het
Larp1b	A	G	3: 40,926,819 (GRCm39)	N184S	probably damaging	Het
Lhx1	A	T	11: 84,410,647 (GRCm39)	S226T	probably benign	Het
Lmo7	A	T	14: 102,124,957 (GRCm39)	Q472L	probably damaging	Het
Mog	G	C	17: 37,328,474 (GRCm39)	N152K	possibly damaging	Het
Mttp	A	G	3: 137,822,166 (GRCm39)		probably null	Het
Mycbp2	A	G	14: 103,489,945 (GRCm39)	V953A	possibly damaging	Het
Myo3a	A	T	2: 22,345,091 (GRCm39)	Y509F	probably damaging	Het
Myo9b	A	G	8: 71,767,836 (GRCm39)	N303S	possibly damaging	Het
Nek3	T	C	8: 22,622,217 (GRCm39)		probably null	Het
Nlrc4	A	T	17: 74,748,926 (GRCm39)	D771E	probably benign	Het
Nup160	A	T	2: 90,552,405 (GRCm39)	N1127I	possibly damaging	Het
Oas1h	A	T	5: 121,000,663 (GRCm39)	N91I	probably damaging	Het
Or13p4	T	A	4: 118,547,389 (GRCm39)	N87Y	probably damaging	Het
Or4c120	A	T	2: 89,000,971 (GRCm39)	V195D	probably benign	Het
Or4c121	G	T	2: 89,024,227 (GRCm39)	S50R	probably damaging	Het
Parp4	T	C	14: 56,827,329 (GRCm39)		probably benign	Het
Pi4ka	G	A	16: 17,099,764 (GRCm39)	C96Y	probably null	Het
Pira2	A	T	7: 3,847,548 (GRCm39)	F47Y	probably damaging	Het
Pkhd1	C	A	1: 20,417,681 (GRCm39)	G2490V	probably damaging	Het
Plekhg1	C	T	10: 3,890,526 (GRCm39)	T394I	probably damaging	Het
Pramel22	G	A	4: 143,382,187 (GRCm39)	Q170*	probably null	Het
Psmd1	T	C	1: 86,019,719 (GRCm39)		probably benign	Het
Rab3ip	A	T	10: 116,775,128 (GRCm39)	C77S	probably benign	Het
Reln	A	T	5: 22,130,211 (GRCm39)	M2700K	probably benign	Het
Rfx1	A	G	8: 84,800,575 (GRCm39)	T59A	probably benign	Het
Ric8b	G	T	10: 84,815,963 (GRCm39)	V405L	probably benign	Het
Rufy3	G	T	5: 88,788,491 (GRCm39)	A479S	probably damaging	Het
Sardh	A	T	2: 27,132,731 (GRCm39)	Y166N	probably damaging	Het
Slamf6	T	G	1: 171,761,975 (GRCm39)	V132G	possibly damaging	Het
Slc12a3	T	G	8: 95,072,505 (GRCm39)	H674Q	possibly damaging	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Srsf9	A	G	5: 115,465,429 (GRCm39)	N21S	possibly damaging	Het
Stkld1	A	T	2: 26,840,102 (GRCm39)	T391S	probably benign	Het
Sumf2	C	A	5: 129,888,755 (GRCm39)	N230K	probably damaging	Het
Tbc1d22a	T	C	15: 86,119,770 (GRCm39)	V22A	possibly damaging	Het
Thsd7b	T	A	1: 129,523,778 (GRCm39)	S194T	possibly damaging	Het
Tnn	T	A	1: 159,924,835 (GRCm39)	Y1173F	probably damaging	Het
Top2a	A	G	11: 98,891,880 (GRCm39)	F1122L	probably damaging	Het
Trappc9	G	A	15: 72,897,816 (GRCm39)	R377W	probably damaging	Het
Trim39	G	A	17: 36,579,746 (GRCm39)	R70W	probably damaging	Het
Ttn	G	A	2: 76,624,605 (GRCm39)	T15289I	probably damaging	Het
Ugt2b38	A	T	5: 87,559,773 (GRCm39)	V373E	probably damaging	Het
Usp54	A	G	14: 20,657,227 (GRCm39)	S24P	probably damaging	Het
Vmn2r27	C	T	6: 124,208,593 (GRCm39)	G51S	probably benign	Het
Zbtb21	A	G	16: 97,753,627 (GRCm39)	S247P	probably benign	Het
Zc3h7b	C	T	15: 81,661,289 (GRCm39)	P376L	probably benign	Het
Zfp251	T	A	15: 76,737,238 (GRCm39)	R613S	probably damaging	Het
Zfp251	C	T	15: 76,737,239 (GRCm39)	R613K	possibly damaging	Het
Zfp91	T	C	19: 12,756,439 (GRCm39)	D135G	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
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
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'- GCCACATCTCAAGTGTCTCTGCTG -3'
(R):5'- TTCTTTGCCCGGAAGTTCGAGTC -3'

Sequencing Primer
(F):5'- CCCTGGAAATGGTCGTCATAG -3'
(R):5'- CGACTGTGAACCAGGAAGTCC -3'

Posted On

2014-04-24