Incidental Mutation 'R0016:Xylt2'
ID 32712
Institutional Source Beutler Lab
Gene Symbol Xylt2
Ensembl Gene ENSMUSG00000020868
Gene Name xylosyltransferase II
Synonyms E030002B02Rik
MMRRC Submission 038311-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.872) question?
Stock # R0016 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 11
Chromosomal Location 94554677-94568341 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 94560466 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 270 (S270P)
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: S270P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112052
Gene: ENSMUSG00000020868
AA Change: S270P

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:Xylo_C 31 97 2.1e-28 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000153485
AA Change: S270P

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000122581
Gene: ENSMUSG00000020868
AA Change: S270P

DomainStartEndE-ValueType
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 0.9366 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.2%
Validation Efficiency 100% (58/58)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 A C 1: 71,333,959 (GRCm39) V1181G probably benign Het
Adamts12 A T 15: 11,217,915 (GRCm39) I291F probably damaging Het
Aspm G C 1: 139,407,282 (GRCm39) Q2056H probably benign Het
C7 A T 15: 5,076,406 (GRCm39) V122E probably benign Het
Casp12 A T 9: 5,352,844 (GRCm39) Q152L probably null Het
Cdh16 T A 8: 105,344,264 (GRCm39) T92S probably benign Het
Chrd G C 16: 20,553,058 (GRCm39) V162L possibly damaging Het
Cpne8 A G 15: 90,385,608 (GRCm39) probably benign Het
Cspg4b T C 13: 113,502,639 (GRCm39) Y115H probably damaging Het
Cyp2j7 T A 4: 96,090,384 (GRCm39) I347F probably damaging Het
Cyp4a10 A T 4: 115,378,304 (GRCm39) Q130L probably damaging Het
Dach1 C T 14: 98,406,184 (GRCm39) G188R probably damaging Het
Dgkd T C 1: 87,845,674 (GRCm39) S294P probably benign Het
Dnah8 A G 17: 30,882,290 (GRCm39) I621V probably benign Het
Dync2h1 A G 9: 7,144,346 (GRCm39) probably benign Het
Echdc1 A T 10: 29,198,417 (GRCm39) probably benign Het
Elovl3 T A 19: 46,120,597 (GRCm39) F30Y probably damaging Het
Fa2h T C 8: 112,120,146 (GRCm39) Y80C probably damaging Het
Fgd3 C T 13: 49,450,085 (GRCm39) D55N probably benign Het
Fhod1 T C 8: 106,058,287 (GRCm39) E823G possibly damaging Het
Gapvd1 A G 2: 34,589,925 (GRCm39) probably benign Het
Gm17067 A T 7: 42,358,046 (GRCm39) I152K probably benign Het
Gvin3 G A 7: 106,202,453 (GRCm39) L264F probably benign Het
Kif27 A G 13: 58,502,528 (GRCm39) V50A probably damaging Het
Kpna2 T C 11: 106,881,912 (GRCm39) T305A probably benign Het
Krtap22-2 A G 16: 88,807,407 (GRCm39) probably benign Het
Lrp2bp T A 8: 46,465,068 (GRCm39) F62L probably damaging Het
Marf1 G A 16: 13,970,129 (GRCm39) H197Y probably damaging Het
Mob3b A G 4: 35,083,947 (GRCm39) F81L probably benign Het
Mon2 C T 10: 122,871,451 (GRCm39) V389M probably damaging Het
Myef2l A T 3: 10,154,379 (GRCm39) M383L possibly damaging Het
Myh8 A G 11: 67,189,351 (GRCm39) K1176E probably damaging Het
Naf1 T C 8: 67,341,707 (GRCm39) probably benign Het
Nckap1l A G 15: 103,384,063 (GRCm39) T554A probably benign Het
Oog3 A G 4: 143,884,641 (GRCm39) Y432H probably damaging Het
Paxbp1 A T 16: 90,832,924 (GRCm39) probably benign Het
Phf20 A T 2: 156,109,114 (GRCm39) K154* probably null Het
Pip4p1 C T 14: 51,166,351 (GRCm39) R213Q probably damaging Het
Plekhj1 T C 10: 80,632,250 (GRCm39) D74G possibly damaging Het
Plpp4 T C 7: 128,925,148 (GRCm39) C128R probably damaging Het
Rcan3 A T 4: 135,145,689 (GRCm39) probably null Het
Sh3rf1 T A 8: 61,827,172 (GRCm39) M642K probably benign Het
Slc7a1 A G 5: 148,271,393 (GRCm39) V522A probably benign Het
Sorbs1 A G 19: 40,303,182 (GRCm39) probably benign Het
Spry2 C T 14: 106,130,731 (GRCm39) V152M probably benign Het
Srgap2 A G 1: 131,277,200 (GRCm39) M349T possibly damaging Het
Stag3 A G 5: 138,289,643 (GRCm39) H271R possibly damaging Het
Stat4 T C 1: 52,107,939 (GRCm39) V136A probably benign Het
Stc2 A T 11: 31,310,177 (GRCm39) D286E probably benign Het
Stk31 T C 6: 49,414,311 (GRCm39) Y482H probably damaging Het
Tasor2 A C 13: 3,635,170 (GRCm39) probably null Het
Ticrr C T 7: 79,343,540 (GRCm39) P1135L probably benign Het
Trim27 A T 13: 21,375,399 (GRCm39) E310V probably benign Het
Uvrag T C 7: 98,641,188 (GRCm39) K284R probably benign Het
Vmn1r78 A C 7: 11,887,279 (GRCm39) S297R probably benign Het
Zfhx3 T C 8: 109,676,810 (GRCm39) M2620T probably benign Het
Zkscan2 C A 7: 123,099,219 (GRCm39) probably benign Het
Zwint T C 10: 72,493,030 (GRCm39) 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
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
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'- TGGCACTTAGCAGGCAGAATGG -3'
(R):5'- AGGTTGAGGTCCAGCATGGTCAAG -3'

Sequencing Primer
(F):5'- CACACCTCGTTGGATAGTCAG -3'
(R):5'- TCCAGCATGGTCAAGCATAAG -3'
Posted On 2013-05-09