Incidental Mutation 'R9415:Pomgnt1'
| ID |
711989 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9415 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
4 |
| Chromosomal Location |
116007700-116017041 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 116013378 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 500
(H500R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000102107
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000106494]
[ENSMUST00000106496]
[ENSMUST00000106498]
[ENSMUST00000120083]
[ENSMUST00000121052]
|
| AlphaFold |
Q91X88 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000106494
AA Change: H478R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000102103
Gene: ENSMUSG00000028700
AA Change: H478R
| Domain | Start | End | E-Value | Type |
|---|
|
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: H467R
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000102105
Gene: ENSMUSG00000028700
AA Change: H467R
| Domain | Start | End | E-Value | Type |
|---|
|
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: H500R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000102107
Gene: ENSMUSG00000028700
AA Change: H500R
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
|
| SMART Domains |
Protein: ENSMUSP00000112751
Gene: ENSMUSG00000028700
AA Change: H500R
| Domain | Start | End | E-Value | Type |
|---|
|
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: H500R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000112911
Gene: ENSMUSG00000028700
AA Change: H500R
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.5%
|
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Anapc1 |
A |
G |
2: 128,476,598 (GRCm39) |
M1340T |
probably benign |
Het |
| Arhgef15 |
A |
G |
11: 68,842,233 (GRCm39) |
L457P |
probably damaging |
Het |
| Arih2 |
A |
T |
9: 108,486,986 (GRCm39) |
C317S |
probably damaging |
Het |
| Asb14 |
A |
T |
14: 26,633,793 (GRCm39) |
T333S |
probably damaging |
Het |
| Atp13a4 |
T |
C |
16: 29,227,821 (GRCm39) |
N1012S |
|
Het |
| Capn9 |
C |
A |
8: 125,332,449 (GRCm39) |
D429E |
probably benign |
Het |
| Celsr1 |
G |
T |
15: 85,917,286 (GRCm39) |
S229* |
probably null |
Het |
| Cntrob |
C |
T |
11: 69,193,741 (GRCm39) |
R803Q |
possibly damaging |
Het |
| Dnah8 |
A |
G |
17: 31,029,297 (GRCm39) |
I4089V |
probably benign |
Het |
| Fam162b |
A |
G |
10: 51,466,155 (GRCm39) |
|
probably null |
Het |
| Fhod3 |
A |
G |
18: 25,102,244 (GRCm39) |
D180G |
probably damaging |
Het |
| Gtf3c4 |
A |
G |
2: 28,723,966 (GRCm39) |
S589P |
possibly damaging |
Het |
| Jcad |
T |
C |
18: 4,673,912 (GRCm39) |
L558P |
probably damaging |
Het |
| Kmt2d |
A |
G |
15: 98,737,586 (GRCm39) |
I5170T |
unknown |
Het |
| Lamb3 |
T |
C |
1: 193,008,319 (GRCm39) |
F251L |
probably benign |
Het |
| Lpxn |
T |
A |
19: 12,802,336 (GRCm39) |
D220E |
probably benign |
Het |
| Mex3a |
T |
A |
3: 88,444,480 (GRCm39) |
F519I |
probably damaging |
Het |
| Mfap1a |
T |
C |
2: 121,337,001 (GRCm39) |
M8V |
probably benign |
Het |
| Mical3 |
T |
A |
6: 120,934,712 (GRCm39) |
D1789V |
probably damaging |
Het |
| Mpdz |
G |
A |
4: 81,235,905 (GRCm39) |
Q1211* |
probably null |
Het |
| Myd88 |
A |
G |
9: 119,167,070 (GRCm39) |
|
probably null |
Het |
| Myof |
T |
A |
19: 37,941,412 (GRCm39) |
K799N |
probably damaging |
Het |
| Naip2 |
T |
A |
13: 100,298,243 (GRCm39) |
S598C |
probably damaging |
Het |
| Ndst4 |
C |
T |
3: 125,518,385 (GRCm39) |
S354L |
probably benign |
Het |
| Ntn4 |
A |
G |
10: 93,480,488 (GRCm39) |
T71A |
probably benign |
Het |
| Omd |
A |
C |
13: 49,745,837 (GRCm39) |
M416L |
probably benign |
Het |
| Oog1 |
G |
C |
12: 87,655,086 (GRCm39) |
L411F |
probably damaging |
Het |
| Or10a3m |
T |
A |
7: 108,313,042 (GRCm39) |
W161R |
probably damaging |
Het |
| Or1e32 |
A |
G |
11: 73,705,143 (GRCm39) |
I255T |
probably damaging |
Het |
| Or56a5 |
T |
G |
7: 104,793,498 (GRCm39) |
M7L |
probably benign |
Het |
| Or7e171-ps1 |
A |
G |
9: 19,853,200 (GRCm39) |
W179R |
probably benign |
Het |
| Pde4dip |
T |
C |
3: 97,660,468 (GRCm39) |
Q670R |
possibly damaging |
Het |
| Pex13 |
C |
A |
11: 23,601,034 (GRCm39) |
G272V |
probably damaging |
Het |
| Pfkl |
A |
T |
10: 77,824,081 (GRCm39) |
V769D |
probably damaging |
Het |
| Pkn3 |
A |
G |
2: 29,968,332 (GRCm39) |
Y10C |
probably benign |
Het |
| Rasef |
T |
C |
4: 73,645,882 (GRCm39) |
T496A |
probably benign |
Het |
| Rgs6 |
A |
G |
12: 83,184,166 (GRCm39) |
S459G |
probably benign |
Het |
| Serpinb6b |
A |
T |
13: 33,159,002 (GRCm39) |
M187L |
|
Het |
| Shcbp1l |
A |
G |
1: 153,321,627 (GRCm39) |
I408M |
possibly damaging |
Het |
| Slc25a45 |
T |
C |
19: 5,934,967 (GRCm39) |
V272A |
probably damaging |
Het |
| Tlr4 |
T |
C |
4: 66,746,160 (GRCm39) |
|
probably null |
Het |
| Unc80 |
A |
T |
1: 66,550,064 (GRCm39) |
N774I |
|
Het |
| Urb2 |
T |
A |
8: 124,756,613 (GRCm39) |
S773R |
possibly damaging |
Het |
| Vmn1r35 |
A |
T |
6: 66,656,115 (GRCm39) |
V185E |
probably damaging |
Het |
| Vps13d |
A |
C |
4: 144,796,527 (GRCm39) |
V3691G |
|
Het |
| Wdtc1 |
A |
G |
4: 133,022,684 (GRCm39) |
V554A |
possibly damaging |
Het |
| Xrn1 |
A |
T |
9: 95,851,527 (GRCm39) |
M182L |
probably damaging |
Het |
| Zfp747 |
T |
C |
7: 126,973,198 (GRCm39) |
H324R |
possibly damaging |
Het |
|
| Other mutations in Pomgnt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
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'- TACAAGGAGGAGCTTGAGCC -3'
(R):5'- TCACAAGGAGGTGATTTGCTG -3'
Sequencing Primer
(F):5'- GTGGCCCACACCAGAAAAGG -3'
(R):5'- GCAGGCAGCATTTTTAATCCTC -3'
|
| Posted On |
2022-05-16 |
Incidental Mutation