Incidental Mutation 'R0715:Pomgnt2'
ID 218498
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 038898-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0715 (G1)
Quality Score 46
Status Validated
Chromosome 9
Chromosomal Location 121810675-121825116 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 121811127 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 551 (K551N)
Ref Sequence ENSEMBL: ENSMUSP00000149753 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043011] [ENSMUST00000084743] [ENSMUST00000213773] [ENSMUST00000214511] [ENSMUST00000214533] [ENSMUST00000214536] [ENSMUST00000217610] [ENSMUST00000216669] [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 probably damaging
Transcript: ENSMUST00000084743
AA Change: K551N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000095868
Gene: ENSMUSG00000066235
AA Change: K551N

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 noncoding transcript
Transcript: ENSMUST00000215008
Predicted Effect probably damaging
Transcript: ENSMUST00000217610
AA Change: K551N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect probably damaging
Transcript: ENSMUST00000216669
AA Change: K551N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect probably benign
Transcript: ENSMUST00000215990
Predicted Effect probably benign
Transcript: ENSMUST00000215084
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 95.8%
Validation Efficiency 98% (61/62)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930438A08Rik A G 11: 58,179,176 (GRCm39) Y170C probably damaging Het
Adcy2 C T 13: 69,036,161 (GRCm39) V167I probably benign Het
Agl A G 3: 116,545,825 (GRCm39) Y1324H probably damaging Het
Arhgef37 G T 18: 61,641,860 (GRCm39) Q170K probably damaging Het
Asah2 A G 19: 31,994,176 (GRCm39) S390P probably damaging Het
Atp8a1 A T 5: 67,932,068 (GRCm39) H240Q probably benign Het
Btbd16 T A 7: 130,390,557 (GRCm39) N151K probably damaging Het
Ccdc73 T A 2: 104,803,499 (GRCm39) probably benign Het
Cecr2 G T 6: 120,735,159 (GRCm39) M21I probably benign Het
Ckap2l T C 2: 129,127,636 (GRCm39) T181A probably benign Het
Col4a3 T C 1: 82,629,879 (GRCm39) probably benign Het
Cplane1 T A 15: 8,252,576 (GRCm39) C1933S probably benign Het
Dnah9 A G 11: 65,972,074 (GRCm39) probably benign Het
Efcab3 T C 11: 104,611,706 (GRCm39) L516P possibly damaging Het
Fat3 T C 9: 16,286,419 (GRCm39) T1035A probably benign Het
Fzd8 A G 18: 9,212,947 (GRCm39) T10A unknown Het
Gm9631 C A 11: 121,833,328 (GRCm39) C636F probably damaging Het
Gp1ba A G 11: 70,531,614 (GRCm39) probably benign Het
Gsk3a A G 7: 24,931,134 (GRCm39) V277A probably damaging Het
H2-M1 T A 17: 36,981,120 (GRCm39) probably benign Het
Hesx1 T A 14: 26,722,809 (GRCm39) W45R probably damaging Het
Il23r T A 6: 67,463,317 (GRCm39) M59L possibly damaging Het
Insc T A 7: 114,444,312 (GRCm39) V433E probably benign Het
Itga8 T C 2: 12,196,053 (GRCm39) probably benign Het
Kif13a T A 13: 46,966,299 (GRCm39) E436V probably damaging Het
Liph A G 16: 21,814,100 (GRCm39) F7S probably benign Het
Lpar2 T C 8: 70,276,823 (GRCm39) V204A probably damaging Het
Lrfn4 T A 19: 4,662,668 (GRCm39) probably null Het
Man2b2 A T 5: 36,983,402 (GRCm39) D182E probably benign Het
Mmp27 T C 9: 7,581,156 (GRCm39) probably benign Het
Mrm1 A G 11: 84,705,639 (GRCm39) probably benign Het
Mtx3 T C 13: 92,986,869 (GRCm39) S271P probably damaging Het
Myh11 A T 16: 14,044,480 (GRCm39) M641K possibly damaging Het
Necab2 A G 8: 120,197,670 (GRCm39) D332G probably damaging Het
Ngfr A G 11: 95,465,065 (GRCm39) I261T possibly damaging Het
Nrap T C 19: 56,345,757 (GRCm39) E617G probably damaging Het
Obscn G T 11: 58,941,306 (GRCm39) T4505K probably benign Het
Or8b37 G T 9: 37,959,123 (GRCm39) V202L probably benign Het
Or8b57 A G 9: 40,003,807 (GRCm39) Y148H probably damaging Het
Osbpl11 T A 16: 33,062,100 (GRCm39) probably benign Het
Otof A G 5: 30,552,041 (GRCm39) V301A probably damaging Het
Phf3 A T 1: 30,850,919 (GRCm39) L1145Q probably damaging Het
Phospho2 T A 2: 69,626,540 (GRCm39) I232N possibly damaging Het
Ptchd3 A G 11: 121,721,984 (GRCm39) T286A possibly damaging Het
Rnf213 A G 11: 119,331,976 (GRCm39) D2396G probably damaging Het
Sh3pxd2b A G 11: 32,373,341 (GRCm39) E836G possibly damaging Het
Simc1 G T 13: 54,673,468 (GRCm39) M605I possibly damaging Het
Slc12a3 G A 8: 95,056,061 (GRCm39) E66K possibly damaging Het
Spg11 T C 2: 121,915,464 (GRCm39) N1060S probably benign Het
Supt5 A T 7: 28,028,462 (GRCm39) W178R probably damaging Het
Tmem41a G T 16: 21,756,740 (GRCm39) F126L probably benign Het
Ube2m T A 7: 12,771,553 (GRCm39) Q35L probably benign Het
Usp33 A G 3: 152,086,211 (GRCm39) D658G probably damaging Het
Vmn2r12 A T 5: 109,238,373 (GRCm39) C456S probably benign Het
Vmn2r81 T A 10: 79,104,434 (GRCm39) D352E probably damaging Het
Zfp516 A G 18: 83,005,388 (GRCm39) Y764C probably damaging Het
Zswim7 A G 11: 62,167,473 (GRCm39) probably benign 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
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
R4428:Pomgnt2 UTSW 9 121,811,320 (GRCm39) missense possibly damaging 0.71
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'- GGTTATTAGCAAGAGCAGATCCCCG -3'
(R):5'- TTCCGAATCTACCAGGACACCAGG -3'

Sequencing Primer
(F):5'- CTCTTCAGAGCTAGAGAAATCTGC -3'
(R):5'- ATGCAATCCATTCGGCGTG -3'
Posted On 2014-08-11