Incidental Mutation 'R0440:Gcnt1'
ID 46728
Institutional Source Beutler Lab
Gene Symbol Gcnt1
Ensembl Gene ENSMUSG00000038843
Gene Name glucosaminyl (N-acetyl) transferase 1, core 2
Synonyms C2 GlcNAcT, IGnT, 5630400D21Rik, beta-1, 6-N-acetylglucosaminyltransferase
MMRRC Submission 038641-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0440 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 19
Chromosomal Location 17303505-17350208 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 17307680 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 15 (T15I)
Ref Sequence ENSEMBL: ENSMUSP00000133935 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000169897] [ENSMUST00000174236]
AlphaFold Q09324
PDB Structure X-ray crystal structure of murine leukocyte-type Core 2 b1,6-N-acetylglucosaminyltransferase (C2GnT-L) [X-RAY DIFFRACTION]
X-ray crystal structure of murine leukocyte-type Core 2 b1,6-N-acetylglucosaminyltransferase (C2GnT-L) in complex with Galb1,3GalNAc [X-RAY DIFFRACTION]
Structure and mechanisim of core 2 beta1,6-n-acetylglucosaminyltransferase: a Metal-ion independent gt-a glycosyltransferase [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000169897
AA Change: T15I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000127835
Gene: ENSMUSG00000038843
AA Change: T15I

DomainStartEndE-ValueType
transmembrane domain 17 34 N/A INTRINSIC
Pfam:Branch 123 392 9.3e-66 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174137
Predicted Effect probably benign
Transcript: ENSMUST00000174236
AA Change: T15I

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000133935
Gene: ENSMUSG00000038843
AA Change: T15I

DomainStartEndE-ValueType
signal peptide 1 36 N/A INTRINSIC
Pfam:Branch 127 396 5.7e-65 PFAM
Meta Mutation Damage Score 0.0771 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.8%
  • 10x: 97.0%
  • 20x: 94.1%
Validation Efficiency 99% (68/69)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this allele display a grossly normal phenotype and are fertile. There are abnormalities in white blood cell counts and in inflammatory response however. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4galt G A 15: 83,112,694 (GRCm39) R30W probably damaging Het
Adam7 T C 14: 68,748,305 (GRCm39) probably null Het
Agl A T 3: 116,552,455 (GRCm39) L1158Q probably damaging Het
Akap9 T C 5: 4,114,569 (GRCm39) S66P probably damaging Het
Akr1c20 T A 13: 4,537,207 (GRCm39) D316V probably benign Het
App C A 16: 84,853,302 (GRCm39) E259* probably null Het
Arhgef4 A G 1: 34,784,529 (GRCm39) probably null Het
Armc9 G A 1: 86,121,984 (GRCm39) probably null Het
Ass1 A T 2: 31,404,831 (GRCm39) N371Y probably damaging Het
Btaf1 C T 19: 36,964,053 (GRCm39) P875S probably damaging Het
Cc2d1b T A 4: 108,483,013 (GRCm39) probably null Het
Ccar1 C T 10: 62,616,236 (GRCm39) V165I possibly damaging Het
Ccdc106 A T 7: 5,063,244 (GRCm39) I250F probably damaging Het
Ccny T C 18: 9,332,917 (GRCm39) I205V probably benign Het
Cfap52 T A 11: 67,844,914 (GRCm39) I52L probably benign Het
Chd8 T A 14: 52,442,283 (GRCm39) T2096S possibly damaging Het
Clstn3 G A 6: 124,428,372 (GRCm39) T423I probably damaging Het
Col13a1 T C 10: 61,703,262 (GRCm39) D440G possibly damaging Het
Dclk3 G A 9: 111,298,231 (GRCm39) V592M probably damaging Het
Ddx31 A T 2: 28,747,144 (GRCm39) I208F probably damaging Het
Dlat A T 9: 50,556,419 (GRCm39) probably null Het
Eml4 T C 17: 83,753,487 (GRCm39) probably null Het
Enpp2 T A 15: 54,710,633 (GRCm39) probably benign Het
Fryl T C 5: 73,244,315 (GRCm39) S38G possibly damaging Het
Gm21834 T C 17: 58,049,121 (GRCm39) T32A possibly damaging Het
Golga2 A G 2: 32,192,945 (GRCm39) D394G probably damaging Het
Gtf3c4 G T 2: 28,730,181 (GRCm39) probably null Het
Igkv4-69 A G 6: 69,261,253 (GRCm39) probably benign Het
Inpp5j T C 11: 3,451,150 (GRCm39) R500G possibly damaging Het
Kif5b A T 18: 6,226,980 (GRCm39) probably benign Het
Klhl36 A G 8: 120,603,290 (GRCm39) E515G probably damaging Het
Lifr C T 15: 7,186,672 (GRCm39) R59* probably null Het
Lrif1 A T 3: 106,641,714 (GRCm39) Q10L possibly damaging Het
Lrp8 A G 4: 107,726,295 (GRCm39) E908G probably damaging Het
Lrrc23 A T 6: 124,747,667 (GRCm39) D307E probably benign Het
Mpv17l T C 16: 13,762,583 (GRCm39) F27L probably damaging Het
Mta3 C T 17: 84,074,016 (GRCm39) A76V probably damaging Het
Muc5ac T A 7: 141,345,771 (GRCm39) Y202* probably null Het
Naprt A G 15: 75,762,918 (GRCm39) probably benign Het
Npr2 T A 4: 43,650,315 (GRCm39) V960D probably damaging Het
Oca2 A T 7: 56,073,100 (GRCm39) Y765F probably benign Het
Or2d2 A T 7: 106,727,939 (GRCm39) H220Q probably benign Het
Plxna2 T A 1: 194,326,712 (GRCm39) Y215* probably null Het
Prdm16 G A 4: 154,561,084 (GRCm39) probably benign Het
Ptn A G 6: 36,721,432 (GRCm39) S3P probably benign Het
Pus10 T C 11: 23,623,331 (GRCm39) probably benign Het
Rad21 A T 15: 51,831,754 (GRCm39) D442E probably benign Het
Rmdn2 A G 17: 79,975,384 (GRCm39) H291R probably damaging Het
Rp1 A G 1: 4,415,863 (GRCm39) S1750P probably damaging Het
Samd4b A T 7: 28,107,585 (GRCm39) I228N probably benign Het
Sdr9c7 G T 10: 127,734,822 (GRCm39) probably benign Het
Slc13a2 T C 11: 78,294,001 (GRCm39) N254D probably benign Het
Slc16a8 T A 15: 79,136,807 (GRCm39) I132F probably damaging Het
Slc18b1 T A 10: 23,694,976 (GRCm39) Y274N probably benign Het
Slc45a2 A T 15: 11,000,903 (GRCm39) M1L probably benign Het
Smc1b A G 15: 84,996,874 (GRCm39) probably benign Het
Stab2 T C 10: 86,785,792 (GRCm39) S617G probably benign Het
Stk10 A G 11: 32,554,190 (GRCm39) M626V probably damaging Het
Synpo2l T G 14: 20,711,466 (GRCm39) I385L possibly damaging Het
Tmprss11d T C 5: 86,486,671 (GRCm39) Y73C probably damaging Het
Ttc21b A G 2: 66,066,726 (GRCm39) V309A probably benign Het
Tubgcp6 A G 15: 88,987,268 (GRCm39) I1235T probably benign Het
Usp8 A G 2: 126,567,310 (GRCm39) I110V probably benign Het
Vps13c G A 9: 67,880,143 (GRCm39) G3442S probably damaging Het
Wdr59 GGGTGGTG GGGTG 8: 112,207,172 (GRCm39) probably benign Het
Zfp207 T A 11: 80,286,333 (GRCm39) probably benign Het
Zfp748 A C 13: 67,701,144 (GRCm39) probably null Het
Other mutations in Gcnt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02700:Gcnt1 APN 19 17,306,780 (GRCm39) missense probably damaging 1.00
IGL02836:Gcnt1 APN 19 17,307,493 (GRCm39) missense probably benign
IGL02977:Gcnt1 APN 19 17,306,738 (GRCm39) missense probably damaging 1.00
IGL03302:Gcnt1 APN 19 17,306,547 (GRCm39) missense probably benign 0.25
magenta UTSW 19 17,306,768 (GRCm39) missense probably damaging 1.00
Violet UTSW 19 17,306,723 (GRCm39) missense probably damaging 1.00
R0183:Gcnt1 UTSW 19 17,306,481 (GRCm39) missense probably benign 0.23
R1159:Gcnt1 UTSW 19 17,307,168 (GRCm39) missense possibly damaging 0.90
R1523:Gcnt1 UTSW 19 17,307,197 (GRCm39) missense probably damaging 1.00
R2240:Gcnt1 UTSW 19 17,306,695 (GRCm39) missense possibly damaging 0.91
R4510:Gcnt1 UTSW 19 17,307,641 (GRCm39) missense probably benign 0.00
R4511:Gcnt1 UTSW 19 17,307,641 (GRCm39) missense probably benign 0.00
R5689:Gcnt1 UTSW 19 17,306,768 (GRCm39) missense probably damaging 1.00
R7765:Gcnt1 UTSW 19 17,306,723 (GRCm39) missense probably damaging 1.00
R8669:Gcnt1 UTSW 19 17,307,143 (GRCm39) missense probably benign 0.38
R8739:Gcnt1 UTSW 19 17,307,437 (GRCm39) missense probably benign 0.00
R9082:Gcnt1 UTSW 19 17,307,559 (GRCm39) missense probably benign 0.00
R9589:Gcnt1 UTSW 19 17,307,422 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- CCTGATGAAAGAGGCACAGTCACG -3'
(R):5'- CCGCTGTTAAACTGGCATCTCACC -3'

Sequencing Primer
(F):5'- CAGTCACGGGTCATGTTTATATAGTC -3'
(R):5'- AAGTTTGTCCCACCACACCA -3'
Posted On 2013-06-11