Incidental Mutation 'R4036:Ndc1'
| ID |
313709 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ndc1
|
| Ensembl Gene |
ENSMUSG00000028614 |
| Gene Name |
NDC1 transmembrane nucleoporin |
| Synonyms |
sks, 2810475A17Rik, Tmem48 |
| MMRRC Submission |
040963-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.947)
|
| Stock # |
R4036 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
107225244-107273543 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 107268269 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Asparagine
at position 602
(D602N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000120365
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030357]
[ENSMUST00000125342]
[ENSMUST00000139560]
[ENSMUST00000149366]
|
| AlphaFold |
Q8VCB1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030357
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000125342
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000139560
AA Change: D602N
PolyPhen 2
Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000120365
Gene: ENSMUSG00000028614
AA Change: D602N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ndc1_Nup
|
20 |
666 |
1.7e-137 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000149366
|
| SMART Domains |
Protein: ENSMUSP00000137180
Gene: ENSMUSG00000028614
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ndc1_Nup
|
19 |
511 |
3.7e-136 |
PFAM |
|
| Meta Mutation Damage Score |
0.4782 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.8%
- 20x: 93.4%
|
| Validation Efficiency |
100% (33/33) |
| MGI Phenotype |
PHENOTYPE: Mutations in this gene produce background sensitive growth rates and skeletal anomalies. Both females and males are sterile. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930544M13Rik |
T |
C |
13: 114,744,205 (GRCm39) |
|
noncoding transcript |
Het |
| Ahctf1 |
T |
C |
1: 179,590,181 (GRCm39) |
Q1364R |
possibly damaging |
Het |
| Anxa2 |
A |
G |
9: 69,395,352 (GRCm39) |
N265S |
probably damaging |
Het |
| Bcan |
A |
G |
3: 87,903,423 (GRCm39) |
|
probably null |
Het |
| Cntln |
A |
G |
4: 84,924,725 (GRCm39) |
Y610C |
probably damaging |
Het |
| Cyp39a1 |
C |
A |
17: 43,987,831 (GRCm39) |
A99E |
probably damaging |
Het |
| Drc1 |
A |
G |
5: 30,504,526 (GRCm39) |
I223V |
probably benign |
Het |
| Eef2kmt |
A |
T |
16: 5,063,135 (GRCm39) |
V335D |
probably damaging |
Het |
| Fanci |
T |
C |
7: 79,094,570 (GRCm39) |
L1167P |
probably damaging |
Het |
| Glb1l3 |
A |
C |
9: 26,740,343 (GRCm39) |
M329R |
probably damaging |
Het |
| Gns |
C |
A |
10: 121,207,095 (GRCm39) |
T72N |
probably damaging |
Het |
| Hspa2 |
T |
C |
12: 76,452,542 (GRCm39) |
V412A |
probably damaging |
Het |
| Klk1b8 |
A |
G |
7: 43,447,511 (GRCm39) |
I9V |
probably null |
Het |
| Map4 |
A |
G |
9: 109,861,283 (GRCm39) |
T216A |
possibly damaging |
Het |
| Metrn |
T |
C |
17: 26,013,984 (GRCm39) |
T281A |
probably benign |
Het |
| Mid1-ps1 |
G |
A |
Y: 90,773,563 (GRCm39) |
|
noncoding transcript |
Het |
| Nsd1 |
A |
G |
13: 55,361,524 (GRCm39) |
D164G |
possibly damaging |
Het |
| Or5ac22 |
T |
A |
16: 59,135,113 (GRCm39) |
H219L |
probably benign |
Het |
| Pcdha8 |
T |
C |
18: 37,125,914 (GRCm39) |
M132T |
probably benign |
Het |
| Pomt2 |
A |
G |
12: 87,158,296 (GRCm39) |
|
probably null |
Het |
| Prrt3 |
AGGGGG |
AGGGG |
6: 113,474,641 (GRCm39) |
|
probably null |
Het |
| Rfx6 |
T |
A |
10: 51,602,842 (GRCm39) |
H786Q |
probably damaging |
Het |
| Scn4a |
A |
C |
11: 106,212,883 (GRCm39) |
L1374R |
possibly damaging |
Het |
| Slc16a9 |
C |
T |
10: 70,110,786 (GRCm39) |
T124M |
probably damaging |
Het |
| Slc46a2 |
A |
T |
4: 59,913,818 (GRCm39) |
F368L |
probably damaging |
Het |
| St18 |
T |
A |
1: 6,898,010 (GRCm39) |
I604K |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,548,497 (GRCm39) |
V31935A |
possibly damaging |
Het |
| Urb1 |
T |
C |
16: 90,584,974 (GRCm39) |
H549R |
probably benign |
Het |
| Vmn1r219 |
A |
G |
13: 23,347,272 (GRCm39) |
M154V |
probably benign |
Het |
| Zfp575 |
G |
A |
7: 24,285,440 (GRCm39) |
S67L |
possibly damaging |
Het |
|
| Other mutations in Ndc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00927:Ndc1
|
APN |
4 |
107,241,977 (GRCm39) |
splice site |
probably benign |
|
|
IGL00929:Ndc1
|
APN |
4 |
107,246,694 (GRCm39) |
missense |
probably benign |
0.23 |
|
IGL01340:Ndc1
|
APN |
4 |
107,231,344 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01376:Ndc1
|
APN |
4 |
107,232,394 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01954:Ndc1
|
APN |
4 |
107,253,001 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02290:Ndc1
|
APN |
4 |
107,252,192 (GRCm39) |
splice site |
probably benign |
|
|
IGL03251:Ndc1
|
APN |
4 |
107,237,856 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R1168:Ndc1
|
UTSW |
4 |
107,253,009 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1541:Ndc1
|
UTSW |
4 |
107,228,485 (GRCm39) |
nonsense |
probably null |
|
|
R1605:Ndc1
|
UTSW |
4 |
107,225,293 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1612:Ndc1
|
UTSW |
4 |
107,252,265 (GRCm39) |
splice site |
probably benign |
|
|
R1716:Ndc1
|
UTSW |
4 |
107,241,992 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3522:Ndc1
|
UTSW |
4 |
107,250,355 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4698:Ndc1
|
UTSW |
4 |
107,268,334 (GRCm39) |
missense |
probably benign |
0.06 |
|
R4794:Ndc1
|
UTSW |
4 |
107,247,419 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5053:Ndc1
|
UTSW |
4 |
107,231,415 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5097:Ndc1
|
UTSW |
4 |
107,231,358 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5158:Ndc1
|
UTSW |
4 |
107,232,362 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5217:Ndc1
|
UTSW |
4 |
107,246,773 (GRCm39) |
missense |
probably benign |
|
|
R5579:Ndc1
|
UTSW |
4 |
107,237,901 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R5666:Ndc1
|
UTSW |
4 |
107,246,723 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R5855:Ndc1
|
UTSW |
4 |
107,240,904 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6180:Ndc1
|
UTSW |
4 |
107,268,395 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R6525:Ndc1
|
UTSW |
4 |
107,225,304 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8065:Ndc1
|
UTSW |
4 |
107,247,595 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8067:Ndc1
|
UTSW |
4 |
107,247,595 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8100:Ndc1
|
UTSW |
4 |
107,240,802 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8428:Ndc1
|
UTSW |
4 |
107,226,017 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8952:Ndc1
|
UTSW |
4 |
107,247,623 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8953:Ndc1
|
UTSW |
4 |
107,238,890 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9489:Ndc1
|
UTSW |
4 |
107,247,863 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9606:Ndc1
|
UTSW |
4 |
107,246,686 (GRCm39) |
missense |
probably damaging |
0.97 |
|
Z1176:Ndc1
|
UTSW |
4 |
107,243,799 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGTCACTAAAGAACACACATGTC -3'
(R):5'- TCGGATGGGTAACTTACTTCAGATG -3'
Sequencing Primer
(F):5'- CGTCAGAGAGCAGCTTTAGAGTC -3'
(R):5'- CTTCAGATGTTCACCAAACGTG -3'
|
| Posted On |
2015-04-30 |
Incidental Mutation