Incidental Mutation 'R5605:Npdc1'
| ID |
439226 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Npdc1
|
| Ensembl Gene |
ENSMUSG00000015094 |
| Gene Name |
neural proliferation, differentiation and control 1 |
| Synonyms |
NPDC-1 |
| MMRRC Submission |
043270-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5605 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
25293062-25299506 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 25298957 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Asparagine
at position 284
(D284N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000071387
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055921]
[ENSMUST00000071442]
[ENSMUST00000133409]
[ENSMUST00000141567]
[ENSMUST00000154809]
|
| AlphaFold |
Q64322 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000055921
AA Change: D293N
PolyPhen 2
Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000049602
Gene: ENSMUSG00000015094
AA Change: D293N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NPDC1
|
1 |
341 |
9.1e-234 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000071442
AA Change: D284N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000071387
Gene: ENSMUSG00000015094
AA Change: D284N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NPDC1
|
1 |
332 |
7.2e-217 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124277
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128144
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131185
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132287
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000133409
AA Change: D226N
PolyPhen 2
Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000117773
Gene: ENSMUSG00000015094
AA Change: D226N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NPDC1
|
1 |
274 |
3.4e-163 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138651
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136138
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144413
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141106
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156824
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000141567
|
| SMART Domains |
Protein: ENSMUSP00000116275
Gene: ENSMUSG00000015094
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NPDC1
|
1 |
231 |
7.8e-141 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154809
|
| SMART Domains |
Protein: ENSMUSP00000123386
Gene: ENSMUSG00000015094
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:NPDC1
|
1 |
142 |
1.8e-88 |
PFAM |
|
| Meta Mutation Damage Score |
0.5505 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.5%
- 20x: 95.9%
|
| Validation Efficiency |
100% (55/55) |
| MGI Phenotype |
PHENOTYPE: Homozygous null mice display no obvious abnormalities in viability, fertility, behavior, or brain morphology. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Afg3l2 |
C |
A |
18: 67,575,425 (GRCm39) |
G83* |
probably null |
Het |
| Arap2 |
A |
T |
5: 62,772,410 (GRCm39) |
M1476K |
possibly damaging |
Het |
| Catsper2 |
G |
A |
2: 121,227,533 (GRCm39) |
R546C |
possibly damaging |
Het |
| Ceacam5 |
T |
C |
7: 17,481,161 (GRCm39) |
F303L |
probably benign |
Het |
| Clvs1 |
A |
G |
4: 9,281,751 (GRCm39) |
D65G |
probably damaging |
Het |
| Coq5 |
T |
C |
5: 115,421,776 (GRCm39) |
|
probably null |
Het |
| D630045J12Rik |
A |
T |
6: 38,168,699 (GRCm39) |
V950E |
probably damaging |
Het |
| Dennd4b |
G |
A |
3: 90,175,675 (GRCm39) |
R148Q |
probably damaging |
Het |
| Dnah7c |
A |
G |
1: 46,837,395 (GRCm39) |
D3936G |
possibly damaging |
Het |
| Doc2b |
T |
C |
11: 75,662,786 (GRCm39) |
E404G |
probably damaging |
Het |
| Dsg1b |
C |
T |
18: 20,532,596 (GRCm39) |
P547S |
probably benign |
Het |
| Eif1ad17 |
T |
A |
12: 87,978,768 (GRCm39) |
C51S |
probably damaging |
Het |
| Erich6 |
A |
G |
3: 58,532,540 (GRCm39) |
Y356H |
probably damaging |
Het |
| Galnt6 |
C |
T |
15: 100,595,106 (GRCm39) |
R465Q |
probably damaging |
Het |
| Gbp5 |
T |
C |
3: 142,207,037 (GRCm39) |
S69P |
probably damaging |
Het |
| Gdpd4 |
T |
C |
7: 97,655,507 (GRCm39) |
V562A |
probably benign |
Het |
| Greb1 |
A |
T |
12: 16,758,727 (GRCm39) |
V663D |
probably damaging |
Het |
| Gtf3c3 |
A |
T |
1: 54,455,085 (GRCm39) |
S593T |
probably benign |
Het |
| H2-Eb1 |
T |
C |
17: 34,528,807 (GRCm39) |
S113P |
probably benign |
Het |
| Herc3 |
C |
T |
6: 58,834,712 (GRCm39) |
R240C |
probably damaging |
Het |
| Iqub |
T |
C |
6: 24,505,620 (GRCm39) |
D96G |
probably benign |
Het |
| Irag1 |
C |
T |
7: 110,545,209 (GRCm39) |
C29Y |
possibly damaging |
Het |
| Kcnt2 |
A |
T |
1: 140,502,481 (GRCm39) |
E858D |
possibly damaging |
Het |
| Lcor |
T |
A |
19: 41,571,302 (GRCm39) |
I165N |
probably damaging |
Het |
| Lrp2 |
C |
T |
2: 69,353,643 (GRCm39) |
R539K |
probably damaging |
Het |
| Lrrc10 |
C |
A |
10: 116,881,805 (GRCm39) |
P160T |
probably damaging |
Het |
| Map3k12 |
G |
T |
15: 102,412,300 (GRCm39) |
D280E |
probably benign |
Het |
| Mcub |
T |
C |
3: 129,710,658 (GRCm39) |
E258G |
probably damaging |
Het |
| Mdn1 |
T |
C |
4: 32,765,664 (GRCm39) |
S5208P |
probably benign |
Het |
| Med20 |
C |
A |
17: 47,934,069 (GRCm39) |
|
probably benign |
Het |
| Mertk |
T |
C |
2: 128,580,227 (GRCm39) |
V227A |
probably benign |
Het |
| Ncstn |
A |
G |
1: 171,908,717 (GRCm39) |
|
probably benign |
Het |
| Nedd4l |
T |
C |
18: 65,307,315 (GRCm39) |
|
probably null |
Het |
| Nfyc |
A |
G |
4: 120,647,686 (GRCm39) |
|
probably benign |
Het |
| Nt5dc1 |
C |
T |
10: 34,279,691 (GRCm39) |
C117Y |
probably benign |
Het |
| Nup88 |
A |
T |
11: 70,834,896 (GRCm39) |
|
probably benign |
Het |
| Or6z7 |
C |
T |
7: 6,483,325 (GRCm39) |
V277M |
probably benign |
Het |
| Pbrm1 |
T |
A |
14: 30,757,949 (GRCm39) |
I193K |
probably benign |
Het |
| Pcsk2 |
T |
C |
2: 143,591,165 (GRCm39) |
|
probably benign |
Het |
| Pdzd2 |
A |
T |
15: 12,592,436 (GRCm39) |
C69* |
probably null |
Het |
| Polr1e |
A |
G |
4: 45,018,723 (GRCm39) |
T18A |
probably benign |
Het |
| Prima1 |
T |
A |
12: 103,166,163 (GRCm39) |
I124F |
probably benign |
Het |
| Rbm34 |
T |
C |
8: 127,676,169 (GRCm39) |
K382R |
probably benign |
Het |
| Rftn1 |
T |
G |
17: 50,354,435 (GRCm39) |
N309T |
probably damaging |
Het |
| Septin1 |
C |
T |
7: 126,814,598 (GRCm39) |
D260N |
probably damaging |
Het |
| Serpina3g |
T |
C |
12: 104,207,299 (GRCm39) |
V154A |
probably damaging |
Het |
| Spef2 |
A |
T |
15: 9,609,606 (GRCm39) |
N1306K |
probably damaging |
Het |
| Stk4 |
T |
C |
2: 163,921,486 (GRCm39) |
F29S |
probably damaging |
Het |
| Stxbp5 |
A |
G |
10: 9,645,490 (GRCm39) |
|
probably benign |
Het |
| Tbl3 |
T |
C |
17: 24,919,733 (GRCm39) |
T774A |
probably benign |
Het |
| Tinag |
A |
G |
9: 76,952,694 (GRCm39) |
Y97H |
probably damaging |
Het |
| Tpm1 |
T |
C |
9: 66,956,317 (GRCm39) |
E33G |
probably damaging |
Het |
| Usp17lb |
T |
C |
7: 104,489,847 (GRCm39) |
E359G |
probably benign |
Het |
| Vmn2r91 |
A |
G |
17: 18,356,763 (GRCm39) |
E810G |
probably damaging |
Het |
| Vwce |
A |
T |
19: 10,635,402 (GRCm39) |
T633S |
possibly damaging |
Het |
| Ylpm1 |
G |
A |
12: 85,075,627 (GRCm39) |
R326H |
probably damaging |
Het |
|
| Other mutations in Npdc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01654:Npdc1
|
APN |
2 |
25,297,649 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
IGL02023:Npdc1
|
APN |
2 |
25,298,032 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02894:Npdc1
|
APN |
2 |
25,298,007 (GRCm39) |
missense |
probably benign |
0.04 |
|
danke
|
UTSW |
2 |
25,296,257 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0650:Npdc1
|
UTSW |
2 |
25,298,021 (GRCm39) |
missense |
probably benign |
0.16 |
|
R1136:Npdc1
|
UTSW |
2 |
25,297,727 (GRCm39) |
missense |
probably benign |
0.09 |
|
R4008:Npdc1
|
UTSW |
2 |
25,298,992 (GRCm39) |
nonsense |
probably null |
|
|
R4724:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4725:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4726:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4728:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4836:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4843:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4882:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5108:Npdc1
|
UTSW |
2 |
25,298,667 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5393:Npdc1
|
UTSW |
2 |
25,298,682 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5572:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5573:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5574:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5630:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5632:Npdc1
|
UTSW |
2 |
25,298,957 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5655:Npdc1
|
UTSW |
2 |
25,297,692 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R6823:Npdc1
|
UTSW |
2 |
25,299,121 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7151:Npdc1
|
UTSW |
2 |
25,299,120 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7400:Npdc1
|
UTSW |
2 |
25,296,257 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8777:Npdc1
|
UTSW |
2 |
25,298,129 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8777-TAIL:Npdc1
|
UTSW |
2 |
25,298,129 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9233:Npdc1
|
UTSW |
2 |
25,296,329 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9391:Npdc1
|
UTSW |
2 |
25,297,979 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R9570:Npdc1
|
UTSW |
2 |
25,298,312 (GRCm39) |
missense |
probably benign |
0.10 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGTGGCCGCTTTTCTCCTG -3'
(R):5'- ATGGTCAAACAGTGGGTTGCG -3'
Sequencing Primer
(F):5'- GTCCCTACCTGCTCGAAAC -3'
(R):5'- TGGGTTGCGCACCTCCATC -3'
|
| Posted On |
2016-10-26 |
Incidental Mutation