Incidental Mutation 'R1565:Xylt2'
ID 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: 0.872) question?
Stock # R1565 (G1)
Quality Score 146
Status Validated
Chromosome 11
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

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

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

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 question?
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
AlleleSourceChrCoordTypePredicted EffectPPH 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

Sequencing Primer
Posted On 2014-04-24