Incidental Mutation 'R5937:Pomgnt1'
ID 462314
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 043242-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5937 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 116007700-116017041 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 116011110 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 220 (T220A)
Ref Sequence ENSEMBL: ENSMUSP00000102103 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000106494] [ENSMUST00000106496] [ENSMUST00000106498] [ENSMUST00000120083] [ENSMUST00000121052]
AlphaFold Q91X88
Predicted Effect probably benign
Transcript: ENSMUST00000106494
AA Change: T220A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000102103
Gene: ENSMUSG00000028700
AA Change: T220A

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 benign
Transcript: ENSMUST00000106496
SMART Domains Protein: ENSMUSP00000102105
Gene: ENSMUSG00000028700

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 benign
Transcript: ENSMUST00000106498
AA Change: T242A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000102107
Gene: ENSMUSG00000028700
AA Change: T242A

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 benign
Transcript: ENSMUST00000120083
AA Change: T242A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000112751
Gene: ENSMUSG00000028700
AA Change: T242A

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 benign
Transcript: ENSMUST00000121052
AA Change: T242A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000112911
Gene: ENSMUSG00000028700
AA Change: T242A

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: ENSMUST00000136855
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135982
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155718
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147612
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133838
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151325
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.3%
  • 20x: 91.5%
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1bg A T 15: 60,791,495 (GRCm39) W314R probably benign Het
Adgrv1 A T 13: 81,255,194 (GRCm39) V6143E probably damaging Het
Agap3 C T 5: 24,682,815 (GRCm39) T261I probably damaging Het
Ano6 T C 15: 95,811,838 (GRCm39) I241T probably damaging Het
Arhgef28 T C 13: 98,076,051 (GRCm39) T1328A probably benign Het
Capn10 C T 1: 92,867,105 (GRCm39) R112W probably damaging Het
Car5a A T 8: 122,666,560 (GRCm39) W46R probably damaging Het
Cntn6 C A 6: 104,810,064 (GRCm39) T582K possibly damaging Het
Ctsh T C 9: 89,943,509 (GRCm39) V60A probably benign Het
Ctsll3 A G 13: 60,947,410 (GRCm39) F259L probably damaging Het
Dennd2b A T 7: 109,156,478 (GRCm39) C91S possibly damaging Het
Fam228a T C 12: 4,787,725 (GRCm39) E16G probably damaging Het
G3bp2 A G 5: 92,203,256 (GRCm39) I388T probably damaging Het
Galnt5 A T 2: 57,928,949 (GRCm39) K926N probably benign Het
Gm10097 G A 10: 5,019,485 (GRCm39) probably benign Het
Gm9978 T A 10: 78,322,675 (GRCm39) noncoding transcript Het
Gria1 A G 11: 57,080,559 (GRCm39) T112A probably benign Het
Hnrnpk A C 13: 58,543,016 (GRCm39) V134G probably damaging Het
Insr A G 8: 3,224,808 (GRCm39) V220A probably benign Het
Lhx4 A G 1: 155,586,023 (GRCm39) I96T probably damaging Het
Lrp1 T C 10: 127,419,745 (GRCm39) T955A possibly damaging Het
Lrtm1 T C 14: 28,743,787 (GRCm39) V85A possibly damaging Het
Man2a2 T C 7: 80,013,251 (GRCm39) Y514C probably damaging Het
Npas1 T A 7: 16,197,187 (GRCm39) D226V probably benign Het
Nrcam G A 12: 44,619,074 (GRCm39) V858I probably benign Het
Or14c40 G T 7: 86,313,684 (GRCm39) L271F probably benign Het
Or5b108 T A 19: 13,168,675 (GRCm39) S215T probably damaging Het
Pde6b G T 5: 108,572,193 (GRCm39) A478S probably benign Het
Pex1 T A 5: 3,674,487 (GRCm39) N789K possibly damaging Het
Plekha6 A G 1: 133,187,839 (GRCm39) D120G possibly damaging Het
Sdr39u1 A T 14: 56,135,364 (GRCm39) I193K probably damaging Het
Sec61a2 C A 2: 5,891,368 (GRCm39) M54I probably benign Het
Sema5a A G 15: 32,574,987 (GRCm39) Y365C probably damaging Het
Sra1 C T 18: 36,804,652 (GRCm39) probably null Het
Taf5 C T 19: 47,070,334 (GRCm39) S640L probably damaging Het
Tas2r140 T A 6: 133,032,236 (GRCm39) H174L probably benign Het
Tmem63a T A 1: 180,788,716 (GRCm39) V351D probably damaging Het
Ttll7 C T 3: 146,649,847 (GRCm39) Q626* probably null Het
Ubn2 T A 6: 38,440,917 (GRCm39) V263E possibly damaging Het
Vmn2r106 C T 17: 20,505,667 (GRCm39) W9* probably null Het
Xrcc3 C G 12: 111,774,406 (GRCm39) C141S probably null Het
Zfp516 T A 18: 82,974,958 (GRCm39) D385E probably 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
R0927:Pomgnt1 UTSW 4 116,009,048 (GRCm39) missense probably damaging 1.00
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
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'- CACCCTGTAGTATCAAGGGAGG -3'
(R):5'- TATCTGCCCAGTGACACTCAG -3'

Sequencing Primer
(F):5'- CCCTGTAGTATCAAGGGAGGAGAAG -3'
(R):5'- CAGTGACACTCAGCCTCTG -3'
Posted On 2017-02-28