Mutagenetix > Incidental Mutation

Incidental Mutation 'R0449:Xylt2'

39540

Institutional Source

Beutler Lab

Gene Symbol

Xylt2

Ensembl Gene

ENSMUSG00000020868

Gene Name

xylosyltransferase II

Synonyms

E030002B02Rik

MMRRC Submission

038649-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.833) question?

Stock #

R0449 (G1)

Quality Score

223

Status

Not validated

Chromosome

Chromosomal Location

94554677-94568341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 94557159 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 111 (Y111H)

Ref Sequence

ENSEMBL: ENSMUSP00000134495 (fasta)

Gene Model

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

AlphaFold

Q9EPL0

Predicted Effect

probably benign
Transcript: ENSMUST00000116349
AA Change: Y714H

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: Y714H

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
AA Change: Y111H

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000134495
Gene: ENSMUSG00000020868
AA Change: Y111H

Domain	Start	End	E-Value	Type
Pfam:Xylo_C	31	97	2.1e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153485

SMART Domains

Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868

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: 99.3%
3x: 98.6%
10x: 97.0%
20x: 94.7%

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb4	A	T	5: 8,989,885 (GRCm39)	R813*	probably null	Het
Accsl	T	A	2: 93,696,419 (GRCm39)	I60F	probably benign	Het
Adam29	C	T	8: 56,325,716 (GRCm39)	G246D	probably benign	Het
Ankrd13c	A	G	3: 157,697,351 (GRCm39)	I319V	probably benign	Het
Bag6	T	G	17: 35,360,442 (GRCm39)	V327G	probably damaging	Het
Barhl1	C	T	2: 28,805,304 (GRCm39)	A130T	probably benign	Het
Bend4	T	C	5: 67,555,583 (GRCm39)	D541G	probably damaging	Het
Birc6	A	C	17: 74,999,290 (GRCm39)	T4673P	probably damaging	Het
Ccdc81	T	C	7: 89,539,679 (GRCm39)	R186G	probably damaging	Het
Cdyl2	A	G	8: 117,309,931 (GRCm39)	F342L	probably damaging	Het
Chd3	C	A	11: 69,248,367 (GRCm39)	V748L	probably damaging	Het
CN725425	G	T	15: 91,123,147 (GRCm39)	R72I	possibly damaging	Het
Col22a1	A	G	15: 71,834,520 (GRCm39)		probably null	Het
Cops3	A	G	11: 59,709,243 (GRCm39)		probably null	Het
Ctnnd1	G	T	2: 84,433,606 (GRCm39)	Q940K	possibly damaging	Het
Dtnb	C	T	12: 3,641,971 (GRCm39)	Q45*	probably null	Het
Efr3a	T	A	15: 65,714,553 (GRCm39)	I280K	probably damaging	Het
Eml6	A	C	11: 29,843,213 (GRCm39)	V167G	probably benign	Het
Fam83c	T	A	2: 155,672,215 (GRCm39)	M407L	probably benign	Het
Fasn	T	C	11: 120,701,894 (GRCm39)	T1862A	probably benign	Het
Fbxl6	A	G	15: 76,420,155 (GRCm39)	I486T	probably damaging	Het
Gpr182	A	G	10: 127,586,565 (GRCm39)	Y129H	probably damaging	Het
Gpr75	A	G	11: 30,842,456 (GRCm39)	S454G	probably damaging	Het
Hectd4	G	A	5: 121,502,653 (GRCm39)		probably null	Het
Hsf4	A	G	8: 106,002,222 (GRCm39)	T411A	probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Il4	A	T	11: 53,509,432 (GRCm39)	M1K	probably null	Het
Ints11	G	T	4: 155,972,405 (GRCm39)	R463L	probably benign	Het
Ints4	G	A	7: 97,178,430 (GRCm39)	E677K	probably damaging	Het
Klk1b11	G	A	7: 43,647,216 (GRCm39)	C50Y	probably damaging	Het
Krt14	C	A	11: 100,098,221 (GRCm39)	G21C	unknown	Het
Krt81	C	A	15: 101,361,508 (GRCm39)	R24L	possibly damaging	Het
L3mbtl2	C	T	15: 81,552,942 (GRCm39)	A125V	probably damaging	Het
Lama3	A	G	18: 12,633,569 (GRCm39)		probably null	Het
Lrrk2	T	C	15: 91,634,478 (GRCm39)	L1414P	probably damaging	Het
Matn2	T	C	15: 34,428,687 (GRCm39)	S684P	probably damaging	Het
Mga	T	A	2: 119,771,862 (GRCm39)	V1574D	probably damaging	Het
Mia2	T	C	12: 59,219,380 (GRCm39)		probably null	Het
Mrpl21	T	A	19: 3,342,459 (GRCm39)		probably benign	Het
Msh5	T	A	17: 35,260,458 (GRCm39)	Q266L	probably benign	Het
Mybpc1	C	A	10: 88,376,822 (GRCm39)	C758F	probably damaging	Het
Myo15a	G	A	11: 60,400,422 (GRCm39)	A2932T	possibly damaging	Het
Nbas	T	A	12: 13,569,109 (GRCm39)	I2021K	probably benign	Het
Neurl4	T	C	11: 69,796,393 (GRCm39)	S424P	probably damaging	Het
Or10j5	T	A	1: 172,784,965 (GRCm39)	V201E	probably damaging	Het
Or2w3	A	C	11: 58,556,789 (GRCm39)	I135L	probably benign	Het
Or6c6	A	G	10: 129,187,103 (GRCm39)	M224V	probably benign	Het
Or7g17	T	C	9: 18,767,945 (GRCm39)	M8T	probably benign	Het
Or7g32	T	A	9: 19,389,388 (GRCm39)	I53F	possibly damaging	Het
Phlpp1	C	T	1: 106,278,308 (GRCm39)	R907W	probably damaging	Het
Pigg	T	C	5: 108,484,277 (GRCm39)	V508A	probably benign	Het
Pkhd1l1	T	G	15: 44,364,915 (GRCm39)	Y685D	probably damaging	Het
Polr3a	A	T	14: 24,534,534 (GRCm39)	I34N	probably damaging	Het
Pramel17	T	C	4: 101,694,158 (GRCm39)	S242G	probably benign	Het
Prex1	A	G	2: 166,411,297 (GRCm39)	V1434A	probably benign	Het
Ptprh	T	A	7: 4,601,005 (GRCm39)	D124V	probably damaging	Het
Rad54b	T	A	4: 11,606,131 (GRCm39)	I513N	probably benign	Het
Rbm12b1	A	G	4: 12,145,507 (GRCm39)	N493S	probably benign	Het
Rfx7	A	T	9: 72,517,586 (GRCm39)		probably null	Het
Serpini1	A	G	3: 75,520,648 (GRCm39)	K82E	probably benign	Het
Slc27a6	T	G	18: 58,742,237 (GRCm39)		probably null	Het
Slc35f2	G	T	9: 53,724,201 (GRCm39)	L358F	probably damaging	Het
Slc45a1	A	C	4: 150,727,762 (GRCm39)	I158M	probably damaging	Het
Slurp2	G	A	15: 74,614,955 (GRCm39)	P62L	probably damaging	Het
Sspo	C	T	6: 48,443,674 (GRCm39)	H1949Y	probably damaging	Het
Tiam1	A	T	16: 89,634,715 (GRCm39)	V865E	possibly damaging	Het
Tlr4	A	C	4: 66,757,857 (GRCm39)	I217L	probably damaging	Het
Top1	C	T	2: 160,554,628 (GRCm39)	R460*	probably null	Het
Trpm3	T	A	19: 22,965,418 (GRCm39)	S1638T	probably benign	Het
Tubgcp5	C	T	7: 55,473,315 (GRCm39)	R798C	probably benign	Het
Vars1	T	G	17: 35,231,703 (GRCm39)		probably null	Het
Zbed5	G	A	5: 129,930,567 (GRCm39)	G172D	probably damaging	Het
Zfp53	C	T	17: 21,729,095 (GRCm39)	T376I	probably benign	Het
Zfp937	G	T	2: 150,081,466 (GRCm39)	V499L	probably benign	Het
Zyx	T	A	6: 42,328,247 (GRCm39)	L152Q	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
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
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'- TGTCCTGACCTGACGAGTGCAAAG -3'
(R):5'- TACTGAGTGGGACCCCAAAGAACG -3'

Sequencing Primer
(F):5'- CTGAGTTATAATGGCAGAGCCAC -3'
(R):5'- CCCAAAGAACGTCTCTTCCG -3'

Posted On

2013-05-23