Incidental Mutation 'R8739:Gcnt1'
ID 663255
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 068586-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8739 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 17303505-17350208 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 17307437 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 96 (M96K)
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: M96K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000127835
Gene: ENSMUSG00000038843
AA Change: M96K

DomainStartEndE-ValueType
transmembrane domain 17 34 N/A INTRINSIC
Pfam:Branch 123 392 9.3e-66 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174236
AA Change: M96K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000133935
Gene: ENSMUSG00000038843
AA Change: M96K

DomainStartEndE-ValueType
signal peptide 1 36 N/A INTRINSIC
Pfam:Branch 127 396 5.7e-65 PFAM
Meta Mutation Damage Score 0.0866 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.9%
  • 20x: 99.6%
Validation Efficiency 100% (59/59)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam24 T C 8: 41,133,480 (GRCm39) V316A possibly damaging Het
Adamts9 T C 6: 92,831,261 (GRCm39) E1364G probably benign Het
Agrn C T 4: 156,257,045 (GRCm39) R1233Q probably benign Het
Ankrd6 A G 4: 32,806,337 (GRCm39) S639P possibly damaging Het
Arid5a A G 1: 36,358,677 (GRCm39) N418S probably benign Het
Cep152 T C 2: 125,461,975 (GRCm39) E69G probably benign Het
Chrnb2 A G 3: 89,669,746 (GRCm39) S109P probably damaging Het
Chuk A G 19: 44,077,135 (GRCm39) S404P probably benign Het
Clec4a3 T C 6: 122,944,508 (GRCm39) Y185H probably damaging Het
Dctd T A 8: 48,591,883 (GRCm39) L149H probably benign Het
Dgkb T A 12: 38,278,323 (GRCm39) probably benign Het
Dhrs13 G C 11: 77,923,492 (GRCm39) R70P possibly damaging Het
Dnah5 G A 15: 28,346,006 (GRCm39) A2449T probably benign Het
Dync1h1 T C 12: 110,581,014 (GRCm39) V247A probably damaging Het
Eef1ece2 G A 16: 20,449,665 (GRCm39) probably benign Het
Espnl T A 1: 91,272,317 (GRCm39) L559Q probably damaging Het
Gak A G 5: 108,739,604 (GRCm39) V627A possibly damaging Het
Ggta1 T C 2: 35,292,572 (GRCm39) D245G probably damaging Het
Hfm1 A T 5: 107,046,371 (GRCm39) F505Y probably damaging Het
Inpp4a A G 1: 37,422,207 (GRCm39) probably benign Het
Kcnj14 C G 7: 45,468,812 (GRCm39) R231P probably damaging Het
Lamc2 A T 1: 153,020,399 (GRCm39) C382* probably null Het
Marveld3 T C 8: 110,688,609 (GRCm39) E44G possibly damaging Het
Mettl17 T C 14: 52,128,848 (GRCm39) F373L possibly damaging Het
Morc3 T A 16: 93,657,398 (GRCm39) L374Q probably damaging Het
Muc16 C T 9: 18,548,594 (GRCm39) D5900N probably benign Het
Myo15a A G 11: 60,368,088 (GRCm39) N283D probably benign Het
Ncapg2 T G 12: 116,379,098 (GRCm39) D197E possibly damaging Het
Nipbl T C 15: 8,332,904 (GRCm39) T2240A probably benign Het
Nrip1 A C 16: 76,088,236 (GRCm39) V1107G possibly damaging Het
Or13a19 T C 7: 139,902,647 (GRCm39) F12L probably damaging Het
Or4d5 G A 9: 40,012,636 (GRCm39) T50I probably benign Het
Or4f52 C A 2: 111,061,834 (GRCm39) M101I probably benign Het
Pcdhb11 T A 18: 37,555,549 (GRCm39) I293K probably damaging Het
Pcsk5 G T 19: 17,432,138 (GRCm39) H1492Q probably benign Het
Pdcd4 T A 19: 53,899,405 (GRCm39) Y131* probably null Het
Pdf T A 8: 107,773,796 (GRCm39) M216L probably damaging Het
Pira13 A T 7: 3,828,188 (GRCm39) S40T Het
Plch1 T C 3: 63,778,106 (GRCm39) H17R possibly damaging Het
Prkdc T G 16: 15,626,068 (GRCm39) S3365A probably benign Het
Rab3c T C 13: 110,397,135 (GRCm39) T44A probably damaging Het
Rad17 T C 13: 100,765,998 (GRCm39) T377A probably benign Het
Rftn1 G T 17: 50,354,408 (GRCm39) A318D probably damaging Het
Rnf215 T G 11: 4,085,959 (GRCm39) probably null Het
Sec31b G A 19: 44,507,620 (GRCm39) T808I probably benign Het
Selenbp1 A T 3: 94,844,601 (GRCm39) D86V probably damaging Het
Smurf2 G T 11: 106,743,322 (GRCm39) Y241* probably null Het
Spint1 T C 2: 119,079,286 (GRCm39) V456A possibly damaging Het
Spmap2 G T 10: 79,419,581 (GRCm39) N240K possibly damaging Het
Stx5a A T 19: 8,725,924 (GRCm39) I175F probably damaging Het
Tenm4 C T 7: 96,555,148 (GRCm39) P2618S probably benign Het
Tfb1m T C 17: 3,569,927 (GRCm39) E313G probably benign Het
Thrb A G 14: 17,963,082 (GRCm38) D15G probably benign Het
Tln2 T C 9: 67,165,555 (GRCm39) K1045R probably damaging Het
Tmx2 T C 2: 84,505,745 (GRCm39) probably benign Het
Trabd T C 15: 88,969,152 (GRCm39) I192T probably damaging Het
Try5 T A 6: 41,288,637 (GRCm39) D194V probably damaging Het
Ttc21a A G 9: 119,796,371 (GRCm39) N1263S probably benign Het
Ttll13 T C 7: 79,902,923 (GRCm39) I197T probably damaging Het
Virma T C 4: 11,540,643 (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
R0440:Gcnt1 UTSW 19 17,307,680 (GRCm39) missense probably benign 0.00
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
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'- TTCTGTCCACGTGAATGCAG -3'
(R):5'- CGGAGGAGACTTTTCTCTTGTCC -3'

Sequencing Primer
(F):5'- GTCCACGTGAATGCAGTAGAAATTC -3'
(R):5'- TGTTTTAAGAATTCATCAGAAGCCTG -3'
Posted On 2021-03-08