Incidental Mutation 'R5409:Pomgnt2'
| ID |
426454 |
| 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 |
042978-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5409 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
9 |
| Chromosomal Location |
121810675-121825116 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 121811303 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 493
(S493T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000149753
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000043011]
[ENSMUST00000084743]
[ENSMUST00000213773]
[ENSMUST00000214511]
[ENSMUST00000214533]
[ENSMUST00000214536]
[ENSMUST00000217610]
[ENSMUST00000216669]
[ENSMUST00000215084]
[ENSMUST00000215990]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000043011
|
| SMART Domains |
Protein: ENSMUSP00000040221
Gene: ENSMUSG00000038233
| Domain | Start | End | E-Value | Type |
|---|
|
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: S493T
PolyPhen 2
Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000095868
Gene: ENSMUSG00000066235
AA Change: S493T
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
possibly damaging
Transcript: ENSMUST00000217610
AA Change: S493T
PolyPhen 2
Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000216669
AA Change: S493T
PolyPhen 2
Score 0.708 (Sensitivity: 0.86; Specificity: 0.92)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000215084
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000215990
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.8%
|
| Validation Efficiency |
|
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca7 |
T |
C |
10: 79,850,154 (GRCm39) |
L2002P |
probably damaging |
Het |
| Acot11 |
C |
T |
4: 106,617,327 (GRCm39) |
G240R |
probably damaging |
Het |
| Adgrl1 |
A |
G |
8: 84,656,371 (GRCm39) |
T230A |
probably damaging |
Het |
| Anapc4 |
A |
G |
5: 53,005,941 (GRCm39) |
E316G |
probably damaging |
Het |
| Asic1 |
GCACC |
GCACCACC |
15: 99,596,684 (GRCm39) |
|
probably benign |
Het |
| Aurka |
T |
G |
2: 172,209,036 (GRCm39) |
Q33P |
possibly damaging |
Het |
| Ccn5 |
G |
A |
2: 163,667,158 (GRCm39) |
C53Y |
probably damaging |
Het |
| Cenpm |
T |
C |
15: 82,118,564 (GRCm39) |
T153A |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,622,452 (GRCm39) |
K538* |
probably null |
Het |
| Clip2 |
G |
A |
5: 134,551,645 (GRCm39) |
T159M |
possibly damaging |
Het |
| Col5a1 |
C |
T |
2: 27,850,457 (GRCm39) |
T518I |
unknown |
Het |
| Dis3 |
A |
T |
14: 99,323,368 (GRCm39) |
M566K |
possibly damaging |
Het |
| Dnah1 |
C |
T |
14: 30,985,212 (GRCm39) |
R3869H |
probably damaging |
Het |
| Gm4775 |
A |
T |
14: 106,338,386 (GRCm39) |
|
noncoding transcript |
Het |
| Hipk2 |
C |
T |
6: 38,706,977 (GRCm39) |
G637D |
probably damaging |
Het |
| Igkv4-61 |
T |
C |
6: 69,394,111 (GRCm39) |
K18E |
possibly damaging |
Het |
| Kcnk4 |
A |
G |
19: 6,903,578 (GRCm39) |
S324P |
probably benign |
Het |
| Larp4 |
T |
C |
15: 99,883,945 (GRCm39) |
C61R |
probably damaging |
Het |
| Nid2 |
T |
C |
14: 19,856,030 (GRCm39) |
F986L |
probably damaging |
Het |
| Or5ac16 |
A |
G |
16: 59,021,920 (GRCm39) |
Y290H |
probably damaging |
Het |
| Or5aq1b |
T |
C |
2: 86,902,214 (GRCm39) |
E88G |
possibly damaging |
Het |
| Or5h22 |
C |
T |
16: 58,894,559 (GRCm39) |
V295I |
possibly damaging |
Het |
| Pgbd5 |
T |
A |
8: 125,098,619 (GRCm39) |
I359F |
probably damaging |
Het |
| Plekhh2 |
T |
C |
17: 84,893,906 (GRCm39) |
|
probably null |
Het |
| Rnf7l |
A |
T |
10: 63,257,403 (GRCm39) |
M39K |
possibly damaging |
Het |
| Rp1l1 |
T |
C |
14: 64,268,070 (GRCm39) |
S1219P |
probably benign |
Het |
| Rprd1b |
T |
A |
2: 157,916,987 (GRCm39) |
F322L |
probably damaging |
Het |
| Sh3rf1 |
G |
A |
8: 61,827,279 (GRCm39) |
V678M |
probably benign |
Het |
| Smpd5 |
C |
A |
15: 76,179,914 (GRCm39) |
T321K |
probably damaging |
Het |
| Spag8 |
T |
A |
4: 43,653,134 (GRCm39) |
|
probably benign |
Het |
| Tanc2 |
T |
C |
11: 105,758,311 (GRCm39) |
C691R |
possibly damaging |
Het |
| Tnc |
A |
C |
4: 63,884,773 (GRCm39) |
M1834R |
probably damaging |
Het |
| Tnc |
A |
T |
4: 63,925,654 (GRCm39) |
Y961N |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,700,893 (GRCm39) |
|
probably benign |
Het |
| Ufl1 |
A |
G |
4: 25,280,706 (GRCm39) |
V47A |
probably damaging |
Het |
| Unc13c |
T |
A |
9: 73,485,672 (GRCm39) |
D1676V |
possibly damaging |
Het |
| Vmn1r65 |
T |
C |
7: 6,012,012 (GRCm39) |
N74S |
possibly damaging |
Het |
| Vmn2r30 |
A |
G |
7: 7,315,547 (GRCm39) |
F762S |
probably damaging |
Het |
|
| Other mutations in Pomgnt2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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 |
|
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'- TCTGCAAAAGGTCCCAGGAG -3'
(R):5'- TGATCCGGGAGAACACAGTC -3'
Sequencing Primer
(F):5'- GGCTCCTGTTAAATATACAGCGGAC -3'
(R):5'- TATCCTGCAGAGCCGAGAG -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation