Incidental Mutation 'R0927:Pomgnt1'
ID 80487
Institutional Source Beutler Lab
Gene Symbol Pomgnt1
Ensembl Gene ENSMUSG00000028700
Gene Name protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase
Synonyms 0610016I07Rik, 4930467B06Rik
MMRRC Submission 039074-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0927 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 116007700-116017041 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 116009048 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 29 (V29D)
Ref Sequence ENSEMBL: ENSMUSP00000102103 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000106494] [ENSMUST00000106496] [ENSMUST00000106498] [ENSMUST00000120083] [ENSMUST00000121052]
AlphaFold Q91X88
Predicted Effect probably damaging
Transcript: ENSMUST00000106494
AA Change: V29D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000102103
Gene: ENSMUSG00000028700
AA Change: V29D

DomainStartEndE-ValueType
transmembrane domain 20 37 N/A INTRINSIC
low complexity region 60 75 N/A INTRINSIC
PDB:2YOQ|C 106 195 6e-10 PDB
Pfam:GNT-I 271 591 3e-52 PFAM
low complexity region 623 636 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000106496
AA Change: V51D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000102105
Gene: ENSMUSG00000028700
AA Change: V51D

DomainStartEndE-ValueType
low complexity region 82 97 N/A INTRINSIC
PDB:2YOP|C 129 217 5e-10 PDB
Pfam:GNT-I 260 580 2.9e-52 PFAM
low complexity region 612 625 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000106498
AA Change: V51D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000102107
Gene: ENSMUSG00000028700
AA Change: V51D

DomainStartEndE-ValueType
low complexity region 82 97 N/A INTRINSIC
PDB:2YOQ|C 129 217 6e-10 PDB
Pfam:GNT-I 293 613 3.2e-52 PFAM
low complexity region 645 658 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000120083
AA Change: V51D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112751
Gene: ENSMUSG00000028700
AA Change: V51D

DomainStartEndE-ValueType
low complexity region 82 97 N/A INTRINSIC
Pfam:ILEI 129 220 8.9e-28 PFAM
Pfam:GNT-I 293 612 1.9e-51 PFAM
low complexity region 645 658 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000121052
AA Change: V51D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112911
Gene: ENSMUSG00000028700
AA Change: V51D

DomainStartEndE-ValueType
low complexity region 82 97 N/A INTRINSIC
PDB:2YOQ|C 129 217 6e-10 PDB
Pfam:GNT-I 293 613 3.2e-52 PFAM
low complexity region 645 658 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127426
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135982
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136855
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155718
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133838
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147612
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.0%
  • 20x: 93.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
PHENOTYPE: Surviving homozygous null mice display a mild dystrophy despite a reduced muscle mass and myofiber number, impaired muscle regeneration and low proliferative activity of satellite cells. Mice homozygous for a gene trap allele show reduced fertility and multiple defects in muscle, eye and brain. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb8 T C 5: 24,607,317 (GRCm39) L363P probably damaging Het
Adam12 T A 7: 133,599,959 (GRCm39) H85L probably damaging Het
Adam34 A T 8: 44,104,621 (GRCm39) H341Q probably damaging Het
Adam34l A T 8: 44,078,160 (GRCm39) M688K probably benign Het
Adam7 A G 14: 68,754,133 (GRCm39) L322P probably damaging Het
Adcy5 T A 16: 34,976,613 (GRCm39) S49T probably benign Het
Arfgap2 T C 2: 91,104,150 (GRCm39) S374P probably benign Het
Arpp19 G A 9: 74,944,967 (GRCm39) probably benign Het
Baz1a T C 12: 54,941,773 (GRCm39) K1478E probably damaging Het
Cdc27 G T 11: 104,396,467 (GRCm39) A812E possibly damaging Het
Chtf8 G A 8: 107,612,150 (GRCm39) T263I probably damaging Het
Clcn6 T C 4: 148,113,849 (GRCm39) N70D probably benign Het
Cntnap5c A T 17: 58,349,553 (GRCm39) T289S possibly damaging Het
Dzip3 T C 16: 48,795,840 (GRCm39) N177S probably damaging Het
Edar G T 10: 58,465,313 (GRCm39) probably null Het
Enam T A 5: 88,641,919 (GRCm39) N244K possibly damaging Het
Fbxw10 A G 11: 62,767,770 (GRCm39) K874E probably damaging Het
Glra3 A G 8: 56,578,239 (GRCm39) E432G possibly damaging Het
Grin3b G A 10: 79,807,062 (GRCm39) R110Q probably benign Het
Herc3 T A 6: 58,845,748 (GRCm39) V423D possibly damaging Het
Ifit2 A T 19: 34,550,984 (GRCm39) T175S probably benign Het
Kcnj8 T G 6: 142,511,627 (GRCm39) I327L possibly damaging Het
Kcns2 A T 15: 34,839,242 (GRCm39) I202F probably benign Het
Kif12 T C 4: 63,087,010 (GRCm39) R305G possibly damaging Het
Limch1 A G 5: 67,154,576 (GRCm39) D362G probably damaging Het
Lrba T C 3: 86,687,540 (GRCm39) I2815T probably damaging Het
Lrrtm1 G T 6: 77,221,843 (GRCm39) M433I probably damaging Het
Myh7b A G 2: 155,462,040 (GRCm39) D312G probably damaging Het
Nrxn1 A T 17: 90,344,758 (GRCm39) I382N probably damaging Het
Nudt6 C T 3: 37,459,502 (GRCm39) R161H probably benign Het
Or10w1 T A 19: 13,631,816 (GRCm39) W8R probably damaging Het
Or11g2 A C 14: 50,856,044 (GRCm39) M122L possibly damaging Het
Or4m1 A T 14: 50,558,186 (GRCm39) Y35* probably null Het
Or7e166 C T 9: 19,624,945 (GRCm39) A274V probably benign Het
Pmf1 A T 3: 88,303,369 (GRCm39) V64D probably damaging Het
Pramel22 T A 4: 143,380,790 (GRCm39) H411L possibly damaging Het
Pramel26 A T 4: 143,539,378 (GRCm39) D38E probably benign Het
Prex1 C T 2: 166,428,457 (GRCm39) A925T probably benign Het
Pus3 A G 9: 35,476,327 (GRCm39) Y72C probably damaging Het
Rnf20 T C 4: 49,642,176 (GRCm39) S247P probably damaging Het
Rnf213 T A 11: 119,305,396 (GRCm39) D542E probably benign Het
Sidt1 T C 16: 44,063,895 (GRCm39) D786G probably benign Het
Sirt6 A T 10: 81,458,475 (GRCm39) D219E probably damaging Het
Slc36a2 A T 11: 55,072,411 (GRCm39) I67N probably damaging Het
Slc47a1 A G 11: 61,264,248 (GRCm39) F57S probably damaging Het
Spg11 T A 2: 121,924,968 (GRCm39) T756S probably damaging Het
Sptbn1 C A 11: 30,071,591 (GRCm39) R1447L probably damaging Het
Tcf7l2 A G 19: 55,907,387 (GRCm39) M340V probably damaging Het
Thap1 T C 8: 26,652,733 (GRCm39) V157A probably benign Het
Ubash3b G A 9: 40,934,853 (GRCm39) Q354* probably null Het
Ubtd1 G A 19: 42,020,460 (GRCm39) W68* probably null Het
Wdr64 G T 1: 175,620,647 (GRCm39) R793L probably damaging Het
Zbtb24 C T 10: 41,327,432 (GRCm39) T106I probably benign Het
Zbtb26 T C 2: 37,326,337 (GRCm39) N233S possibly damaging Het
Zcchc24 A T 14: 25,757,585 (GRCm39) N99K possibly damaging Het
Other mutations in Pomgnt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00534:Pomgnt1 APN 4 116,009,958 (GRCm39) missense probably damaging 1.00
IGL02001:Pomgnt1 APN 4 116,010,105 (GRCm39) nonsense probably null
IGL02582:Pomgnt1 APN 4 116,015,747 (GRCm39) missense probably damaging 1.00
pomegranate UTSW 4 116,012,087 (GRCm39) missense probably damaging 1.00
R0206:Pomgnt1 UTSW 4 116,015,757 (GRCm39) critical splice donor site probably null
R0688:Pomgnt1 UTSW 4 116,013,086 (GRCm39) missense probably damaging 1.00
R0890:Pomgnt1 UTSW 4 116,009,382 (GRCm39) missense probably benign 0.25
R1942:Pomgnt1 UTSW 4 116,012,472 (GRCm39) splice site probably null
R1983:Pomgnt1 UTSW 4 116,009,117 (GRCm39) missense probably benign 0.12
R1983:Pomgnt1 UTSW 4 116,009,066 (GRCm39) missense probably damaging 1.00
R2034:Pomgnt1 UTSW 4 116,015,124 (GRCm39) missense possibly damaging 0.87
R3721:Pomgnt1 UTSW 4 116,010,740 (GRCm39) splice site probably benign
R3774:Pomgnt1 UTSW 4 116,011,325 (GRCm39) missense probably damaging 1.00
R3775:Pomgnt1 UTSW 4 116,011,325 (GRCm39) missense probably damaging 1.00
R3815:Pomgnt1 UTSW 4 116,011,139 (GRCm39) critical splice donor site probably null
R3816:Pomgnt1 UTSW 4 116,011,139 (GRCm39) critical splice donor site probably null
R3817:Pomgnt1 UTSW 4 116,011,139 (GRCm39) critical splice donor site probably null
R3818:Pomgnt1 UTSW 4 116,011,139 (GRCm39) critical splice donor site probably null
R4447:Pomgnt1 UTSW 4 116,010,120 (GRCm39) missense possibly damaging 0.75
R4583:Pomgnt1 UTSW 4 116,015,691 (GRCm39) missense probably benign 0.03
R4616:Pomgnt1 UTSW 4 116,012,087 (GRCm39) missense probably damaging 1.00
R4690:Pomgnt1 UTSW 4 116,012,707 (GRCm39) missense probably damaging 1.00
R4717:Pomgnt1 UTSW 4 116,011,412 (GRCm39) missense possibly damaging 0.50
R4719:Pomgnt1 UTSW 4 116,012,972 (GRCm39) missense probably damaging 1.00
R4747:Pomgnt1 UTSW 4 116,013,396 (GRCm39) missense probably damaging 1.00
R5108:Pomgnt1 UTSW 4 116,013,453 (GRCm39) intron probably benign
R5569:Pomgnt1 UTSW 4 116,013,164 (GRCm39) missense probably damaging 1.00
R5821:Pomgnt1 UTSW 4 116,012,933 (GRCm39) missense probably benign 0.16
R5937:Pomgnt1 UTSW 4 116,011,110 (GRCm39) missense probably benign 0.01
R6052:Pomgnt1 UTSW 4 116,008,799 (GRCm39) missense possibly damaging 0.91
R6745:Pomgnt1 UTSW 4 116,011,080 (GRCm39) missense probably damaging 0.97
R6949:Pomgnt1 UTSW 4 116,011,351 (GRCm39) missense probably damaging 0.97
R7503:Pomgnt1 UTSW 4 116,009,949 (GRCm39) missense possibly damaging 0.76
R7876:Pomgnt1 UTSW 4 116,015,106 (GRCm39) missense probably damaging 1.00
R8464:Pomgnt1 UTSW 4 116,009,348 (GRCm39) missense probably damaging 1.00
R9415:Pomgnt1 UTSW 4 116,013,378 (GRCm39) missense probably damaging 1.00
T0722:Pomgnt1 UTSW 4 115,994,624 (GRCm39) unclassified probably benign
T0975:Pomgnt1 UTSW 4 115,994,624 (GRCm39) unclassified probably benign
Z1177:Pomgnt1 UTSW 4 116,009,906 (GRCm39) missense possibly damaging 0.88
Predicted Primers PCR Primer
(F):5'- AGGGAACATTCTCTGGGAGATGGC -3'
(R):5'- ATTGTAACAGGCGTGGGCGATGAC -3'

Sequencing Primer
(F):5'- GCCACAAATCCGTGTCCTTATTG -3'
(R):5'- GGCGATGACTCACTAGCAG -3'
Posted On 2013-11-07