Incidental Mutation 'R4428:Pomgnt2'
ID 328279
Institutional Source Beutler Lab
Gene Symbol Pomgnt2
Ensembl Gene ENSMUSG00000066235
Gene Name protein O-linked mannose beta 1,4-N-acetylglucosaminyltransferase 2
Synonyms Gtdc2, C85492
MMRRC Submission 041698-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4428 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 121810675-121825116 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 121811320 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 487 (E487G)
Ref Sequence ENSEMBL: ENSMUSP00000149753 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043011] [ENSMUST00000084743] [ENSMUST00000213773] [ENSMUST00000214511] [ENSMUST00000214533] [ENSMUST00000214536] [ENSMUST00000216669] [ENSMUST00000217610] [ENSMUST00000215990] [ENSMUST00000215084]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000043011
SMART Domains Protein: ENSMUSP00000040221
Gene: ENSMUSG00000038233

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
low complexity region 183 194 N/A INTRINSIC
Pfam:FAM198 220 544 1.3e-150 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000084743
AA Change: E487G

PolyPhen 2 Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000095868
Gene: ENSMUSG00000066235
AA Change: E487G

DomainStartEndE-ValueType
signal peptide 1 16 N/A INTRINSIC
low complexity region 29 38 N/A INTRINSIC
Pfam:DUF563 162 395 1.7e-25 PFAM
low complexity region 462 475 N/A INTRINSIC
SCOP:d1f6fb2 482 580 6e-9 SMART
Blast:FN3 486 570 2e-49 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000213773
Predicted Effect probably benign
Transcript: ENSMUST00000214511
Predicted Effect probably benign
Transcript: ENSMUST00000214533
Predicted Effect probably benign
Transcript: ENSMUST00000214536
Predicted Effect possibly damaging
Transcript: ENSMUST00000216669
AA Change: E487G

PolyPhen 2 Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
Predicted Effect possibly damaging
Transcript: ENSMUST00000217610
AA Change: E487G

PolyPhen 2 Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000215008
Predicted Effect probably benign
Transcript: ENSMUST00000215990
Predicted Effect probably benign
Transcript: ENSMUST00000215084
Meta Mutation Damage Score 0.0847 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (46/46)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased birth body size and complete neonatal lethality associated with abnormal basal lamina formation and a neuronal migration defect due to a lack of laminin-binding glycans on alpha-dystroglycan. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik G T 5: 64,056,182 (GRCm39) probably benign Het
Abcc1 T A 16: 14,263,164 (GRCm39) V708E probably damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Ccdc18 A G 5: 108,283,943 (GRCm39) Y82C probably benign Het
Cd82 T C 2: 93,250,214 (GRCm39) Y266C probably damaging Het
Chrna4 A G 2: 180,670,413 (GRCm39) S448P probably damaging Het
Cldn8 A C 16: 88,359,619 (GRCm39) M102R probably damaging Het
Cmpk1 T C 4: 114,820,559 (GRCm39) E180G probably benign Het
Dock8 T C 19: 25,177,863 (GRCm39) I2066T probably damaging Het
Dock8 T C 19: 25,042,754 (GRCm39) V112A probably benign Het
Fgf3 T C 7: 144,394,444 (GRCm39) V86A probably damaging Het
Frem2 A G 3: 53,561,759 (GRCm39) I916T probably benign Het
Gsk3b T A 16: 38,014,298 (GRCm39) L252Q probably damaging Het
Kif18a A G 2: 109,118,466 (GRCm39) T94A probably damaging Het
Klhdc1 T A 12: 69,315,000 (GRCm39) probably benign Het
Klhl25 T A 7: 75,515,162 (GRCm39) F23I probably damaging Het
Mapk7 T C 11: 61,380,055 (GRCm39) D701G possibly damaging Het
Mbd5 A T 2: 49,169,776 (GRCm39) Q47L possibly damaging Het
Nrcam A G 12: 44,623,558 (GRCm39) D1049G possibly damaging Het
Olfml2a G T 2: 38,831,755 (GRCm39) M111I probably damaging Het
Or3a1c T C 11: 74,046,025 (GRCm39) F15S probably damaging Het
Pld2 A T 11: 70,432,160 (GRCm39) H93L probably damaging Het
Psg17 G T 7: 18,550,717 (GRCm39) N379K probably benign Het
Rfk T A 19: 17,375,959 (GRCm39) H84Q possibly damaging Het
Scn8a A G 15: 100,881,784 (GRCm39) Y617C probably damaging Het
Sema3d T C 5: 12,498,087 (GRCm39) F31S probably benign Het
Shq1 T C 6: 100,647,889 (GRCm39) Y45C probably damaging Het
Siglecg C T 7: 43,067,350 (GRCm39) P639L possibly damaging Het
Skp2 A T 15: 9,117,034 (GRCm39) N325K probably benign Het
Sost G A 11: 101,857,670 (GRCm39) P44S probably damaging Het
Sp8 T A 12: 118,812,938 (GRCm39) S264R possibly damaging Het
Sun1 T C 5: 139,220,230 (GRCm39) probably benign Het
Tardbp A G 4: 148,709,659 (GRCm39) V54A possibly damaging Het
Tert T A 13: 73,775,594 (GRCm39) F115Y probably damaging Het
Tmem181a T A 17: 6,346,061 (GRCm39) L185H probably damaging Het
Tmem68 A T 4: 3,569,534 (GRCm39) I52K probably benign Het
Trhde A T 10: 114,339,028 (GRCm39) L594Q probably damaging Het
Umps A C 16: 33,781,956 (GRCm39) V322G probably damaging Het
Vmn2r109 T C 17: 20,773,286 (GRCm39) D445G probably benign Het
Vmn2r22 T C 6: 123,614,817 (GRCm39) T258A possibly damaging Het
Vmn2r4 C T 3: 64,322,590 (GRCm39) G43E probably damaging Het
Other mutations in Pomgnt2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00596:Pomgnt2 APN 9 121,812,191 (GRCm39) missense probably benign 0.03
IGL01911:Pomgnt2 APN 9 121,811,854 (GRCm39) missense probably benign 0.05
IGL01943:Pomgnt2 APN 9 121,811,536 (GRCm39) missense probably benign 0.06
IGL02955:Pomgnt2 APN 9 121,811,956 (GRCm39) missense probably damaging 1.00
H8441:Pomgnt2 UTSW 9 121,811,650 (GRCm39) missense probably damaging 1.00
R0080:Pomgnt2 UTSW 9 121,811,326 (GRCm39) missense probably damaging 1.00
R0082:Pomgnt2 UTSW 9 121,811,326 (GRCm39) missense probably damaging 1.00
R0602:Pomgnt2 UTSW 9 121,811,339 (GRCm39) missense probably benign 0.02
R0715:Pomgnt2 UTSW 9 121,811,127 (GRCm39) missense probably damaging 1.00
R1491:Pomgnt2 UTSW 9 121,811,326 (GRCm39) missense probably damaging 1.00
R1908:Pomgnt2 UTSW 9 121,811,257 (GRCm39) missense possibly damaging 0.89
R1909:Pomgnt2 UTSW 9 121,811,257 (GRCm39) missense possibly damaging 0.89
R2041:Pomgnt2 UTSW 9 121,811,354 (GRCm39) missense probably benign 0.00
R4578:Pomgnt2 UTSW 9 121,812,131 (GRCm39) missense probably damaging 1.00
R4910:Pomgnt2 UTSW 9 121,812,013 (GRCm39) missense probably benign 0.19
R4937:Pomgnt2 UTSW 9 121,811,620 (GRCm39) missense probably benign 0.05
R5409:Pomgnt2 UTSW 9 121,811,303 (GRCm39) missense possibly damaging 0.71
R6090:Pomgnt2 UTSW 9 121,811,863 (GRCm39) missense probably damaging 1.00
R6596:Pomgnt2 UTSW 9 121,811,320 (GRCm39) missense possibly damaging 0.71
R7152:Pomgnt2 UTSW 9 121,812,589 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTGCAGGGTCAGCATGTAAG -3'
(R):5'- TGATCCGGGAGAACACAGTCAC -3'

Sequencing Primer
(F):5'- GCATGTAAGGCACATACGTGTTCTC -3'
(R):5'- TATCCTGCAGAGCCGAGAG -3'
Posted On 2015-07-07