Incidental Mutation 'R3938:Nup54'
| ID |
307266 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nup54
|
| Ensembl Gene |
ENSMUSG00000034826 |
| Gene Name |
nucleoporin 54 |
| Synonyms |
3110079L04Rik, 54kDa |
| MMRRC Submission |
040825-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.963)
|
| Stock # |
R3938 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
92563399-92583078 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 92565388 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Threonine
at position 443
(M443T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000046540
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038514]
[ENSMUST00000113083]
[ENSMUST00000117108]
[ENSMUST00000118106]
[ENSMUST00000119587]
[ENSMUST00000120193]
[ENSMUST00000120416]
[ENSMUST00000152041]
[ENSMUST00000121096]
|
| AlphaFold |
Q8BTS4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000038514
AA Change: M443T
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000046540
Gene: ENSMUSG00000034826
AA Change: M443T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
109 |
N/A |
INTRINSIC |
|
Pfam:Nup54
|
303 |
441 |
4.8e-49 |
PFAM |
|
PDB:3T98|C
|
445 |
494 |
2e-26 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000113083
|
| SMART Domains |
Protein: ENSMUSP00000108706
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
4.4e-65 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117108
|
| SMART Domains |
Protein: ENSMUSP00000113041
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
1.9e-65 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118106
|
| SMART Domains |
Protein: ENSMUSP00000114083
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
9e-66 |
PFAM |
|
low complexity region
|
298 |
309 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000119587
|
| SMART Domains |
Protein: ENSMUSP00000112648
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
4e-65 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000120193
|
| SMART Domains |
Protein: ENSMUSP00000113074
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
8.4e-66 |
PFAM |
|
low complexity region
|
298 |
309 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000120416
|
| SMART Domains |
Protein: ENSMUSP00000113493
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
3.1e-65 |
PFAM |
|
low complexity region
|
298 |
309 |
N/A |
INTRINSIC |
|
low complexity region
|
366 |
373 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123694
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129222
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000126281
|
| SMART Domains |
Protein: ENSMUSP00000116110
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ART
|
1 |
190 |
3e-53 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152041
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000121096
|
| SMART Domains |
Protein: ENSMUSP00000113510
Gene: ENSMUSG00000034842
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:ART
|
29 |
251 |
1.8e-65 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000138003
|
| Meta Mutation Damage Score |
0.4769 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.1%
|
| Validation Efficiency |
98% (57/58) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts1 |
C |
T |
16: 85,592,507 (GRCm39) |
V634M |
possibly damaging |
Het |
| Arid4b |
A |
T |
13: 14,361,513 (GRCm39) |
N659I |
probably benign |
Het |
| BC049715 |
T |
C |
6: 136,817,453 (GRCm39) |
I231T |
possibly damaging |
Het |
| Bmp4 |
T |
C |
14: 46,621,536 (GRCm39) |
Y336C |
probably damaging |
Het |
| Ccdc30 |
G |
A |
4: 119,209,870 (GRCm39) |
T293I |
probably benign |
Het |
| Chd5 |
A |
T |
4: 152,461,512 (GRCm39) |
T1275S |
probably benign |
Het |
| Chtf8 |
A |
T |
8: 107,612,537 (GRCm39) |
M134K |
probably benign |
Het |
| Col11a2 |
A |
T |
17: 34,258,599 (GRCm39) |
|
probably benign |
Het |
| Cyp8b1 |
A |
G |
9: 121,744,684 (GRCm39) |
V216A |
probably benign |
Het |
| Dnah8 |
C |
T |
17: 31,073,911 (GRCm39) |
T4527M |
probably damaging |
Het |
| Elavl3 |
A |
G |
9: 21,930,040 (GRCm39) |
V288A |
probably damaging |
Het |
| Erap1 |
T |
A |
13: 74,816,147 (GRCm39) |
L92Q |
probably damaging |
Het |
| Exoc3l |
G |
T |
8: 106,020,037 (GRCm39) |
P296H |
probably damaging |
Het |
| Fcgbpl1 |
C |
T |
7: 27,853,719 (GRCm39) |
P1561L |
probably damaging |
Het |
| Foxl3 |
A |
T |
5: 138,806,723 (GRCm39) |
N78Y |
probably damaging |
Het |
| Hacl1 |
T |
C |
14: 31,356,148 (GRCm39) |
|
probably benign |
Het |
| Hrnr |
T |
A |
3: 93,230,162 (GRCm39) |
N133K |
probably benign |
Het |
| Itgax |
G |
T |
7: 127,735,445 (GRCm39) |
R504S |
possibly damaging |
Het |
| Itgb4 |
A |
G |
11: 115,896,752 (GRCm39) |
S1461G |
possibly damaging |
Het |
| Klkb1 |
G |
T |
8: 45,735,838 (GRCm39) |
T175K |
probably damaging |
Het |
| Lrrk2 |
A |
T |
15: 91,596,983 (GRCm39) |
D525V |
possibly damaging |
Het |
| Lrrk2 |
C |
A |
15: 91,662,707 (GRCm39) |
T1912K |
probably damaging |
Het |
| Mdga1 |
G |
T |
17: 30,076,596 (GRCm39) |
Q59K |
probably damaging |
Het |
| Mpp4 |
A |
G |
1: 59,163,842 (GRCm39) |
V466A |
possibly damaging |
Het |
| Myh6 |
T |
C |
14: 55,200,512 (GRCm39) |
D203G |
probably benign |
Het |
| Myo5b |
T |
C |
18: 74,849,108 (GRCm39) |
S1116P |
probably damaging |
Het |
| Nemp1 |
T |
C |
10: 127,531,342 (GRCm39) |
L311P |
probably damaging |
Het |
| Nup205 |
A |
G |
6: 35,196,677 (GRCm39) |
R1138G |
probably damaging |
Het |
| Peak1 |
T |
C |
9: 56,167,649 (GRCm39) |
E93G |
probably benign |
Het |
| Pirb |
A |
T |
7: 3,720,637 (GRCm39) |
L287Q |
probably benign |
Het |
| Plekhj1 |
A |
G |
10: 80,633,609 (GRCm39) |
I76T |
probably damaging |
Het |
| Poll |
A |
G |
19: 45,546,857 (GRCm39) |
|
probably benign |
Het |
| Ppp1r3a |
A |
T |
6: 14,719,073 (GRCm39) |
S614T |
probably damaging |
Het |
| Pygm |
A |
T |
19: 6,442,980 (GRCm39) |
I556F |
probably benign |
Het |
| Ranbp2 |
T |
C |
10: 58,312,294 (GRCm39) |
F1005L |
probably benign |
Het |
| Rcor3 |
G |
T |
1: 191,785,385 (GRCm39) |
T361K |
possibly damaging |
Het |
| Robo4 |
A |
G |
9: 37,313,313 (GRCm39) |
|
probably benign |
Het |
| Rps15 |
T |
C |
10: 80,129,673 (GRCm39) |
V96A |
probably benign |
Het |
| Rrm2 |
T |
A |
12: 24,759,431 (GRCm39) |
N55K |
probably damaging |
Het |
| Shank2 |
T |
C |
7: 143,682,112 (GRCm39) |
Y382H |
probably benign |
Het |
| Slc25a10 |
G |
T |
11: 120,382,819 (GRCm39) |
E3* |
probably null |
Het |
| Slc7a8 |
T |
A |
14: 54,973,298 (GRCm39) |
E223V |
probably benign |
Het |
| Snx13 |
A |
G |
12: 35,194,096 (GRCm39) |
K880E |
probably benign |
Het |
| Spinkl |
T |
G |
18: 44,301,216 (GRCm39) |
M41L |
probably benign |
Het |
| Srp54a |
A |
C |
12: 55,136,042 (GRCm39) |
N19T |
probably benign |
Het |
| Sun2 |
T |
C |
15: 79,618,356 (GRCm39) |
K268E |
probably benign |
Het |
| Sytl1 |
G |
A |
4: 132,982,935 (GRCm39) |
Q359* |
probably null |
Het |
| Tlr6 |
A |
T |
5: 65,110,938 (GRCm39) |
F656L |
probably damaging |
Het |
| Tmem185a |
C |
T |
X: 69,505,792 (GRCm39) |
|
probably null |
Het |
| Tmem45a2 |
C |
T |
16: 56,859,398 (GRCm39) |
D278N |
probably benign |
Het |
| Trav7-1 |
T |
C |
14: 52,892,791 (GRCm39) |
|
probably benign |
Het |
| Trpc2 |
T |
A |
7: 101,742,781 (GRCm39) |
M597K |
probably damaging |
Het |
| Ttc21a |
A |
G |
9: 119,779,882 (GRCm39) |
|
probably benign |
Het |
| Usp9y |
C |
T |
Y: 1,313,741 (GRCm39) |
M2188I |
probably damaging |
Het |
| Utrn |
C |
A |
10: 12,625,774 (GRCm39) |
|
probably null |
Het |
| Vmn1r35 |
T |
A |
6: 66,656,057 (GRCm39) |
R204S |
probably damaging |
Het |
| Zfp955b |
T |
A |
17: 33,524,390 (GRCm39) |
Y59F |
probably damaging |
Het |
|
| Other mutations in Nup54 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00491:Nup54
|
APN |
5 |
92,565,344 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01526:Nup54
|
APN |
5 |
92,565,334 (GRCm39) |
missense |
probably benign |
0.12 |
|
IGL01924:Nup54
|
APN |
5 |
92,572,294 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL02248:Nup54
|
APN |
5 |
92,576,188 (GRCm39) |
splice site |
probably null |
|
|
IGL02253:Nup54
|
APN |
5 |
92,565,310 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02508:Nup54
|
APN |
5 |
92,565,398 (GRCm39) |
nonsense |
probably null |
|
|
IGL02721:Nup54
|
APN |
5 |
92,565,716 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
IGL03150:Nup54
|
APN |
5 |
92,576,023 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0189:Nup54
|
UTSW |
5 |
92,570,423 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1401:Nup54
|
UTSW |
5 |
92,576,080 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1862:Nup54
|
UTSW |
5 |
92,567,426 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R4171:Nup54
|
UTSW |
5 |
92,565,343 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R4574:Nup54
|
UTSW |
5 |
92,573,641 (GRCm39) |
missense |
probably benign |
0.17 |
|
R5372:Nup54
|
UTSW |
5 |
92,565,716 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6003:Nup54
|
UTSW |
5 |
92,570,853 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6191:Nup54
|
UTSW |
5 |
92,572,153 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6197:Nup54
|
UTSW |
5 |
92,578,663 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R7861:Nup54
|
UTSW |
5 |
92,578,952 (GRCm39) |
missense |
unknown |
|
|
R8005:Nup54
|
UTSW |
5 |
92,576,006 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8016:Nup54
|
UTSW |
5 |
92,582,176 (GRCm39) |
missense |
unknown |
|
|
R8439:Nup54
|
UTSW |
5 |
92,573,605 (GRCm39) |
missense |
probably benign |
0.22 |
|
R8709:Nup54
|
UTSW |
5 |
92,570,267 (GRCm39) |
intron |
probably benign |
|
|
R9711:Nup54
|
UTSW |
5 |
92,582,218 (GRCm39) |
missense |
unknown |
|
|
Z1177:Nup54
|
UTSW |
5 |
92,582,138 (GRCm39) |
missense |
unknown |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TCTCCATTCTCATGACCAGGAG -3'
(R):5'- TGGTTCAAGGTGGTCAGTACAG -3'
Sequencing Primer
(F):5'- CTCATGACCAGGAGAGTATTTCTGC -3'
(R):5'- GTGGTCAGTACAGTTGTCCCATC -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation