Incidental Mutation 'R4725:Npdc1'
| ID |
358380 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Npdc1
|
| Ensembl Gene |
ENSMUSG00000015094 |
| Gene Name |
neural proliferation, differentiation and control 1 |
| Synonyms |
NPDC-1 |
| MMRRC Submission |
041960-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4725 (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: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
96% (64/67) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5830454E08Rik |
T |
C |
9: 120,406,769 (GRCm39) |
|
probably benign |
Het |
| Adamts20 |
T |
C |
15: 94,249,643 (GRCm39) |
E458G |
probably damaging |
Het |
| Adgrl3 |
T |
C |
5: 81,914,052 (GRCm39) |
I1220T |
possibly damaging |
Het |
| Aldh1a1 |
T |
A |
19: 20,617,445 (GRCm39) |
M459K |
probably benign |
Het |
| Bmal1 |
C |
A |
7: 112,903,566 (GRCm39) |
P454Q |
possibly damaging |
Het |
| Camta1 |
A |
G |
4: 151,232,953 (GRCm39) |
V240A |
probably benign |
Het |
| Ccdc88b |
C |
T |
19: 6,834,481 (GRCm39) |
G149R |
probably damaging |
Het |
| Ceacam5 |
T |
C |
7: 17,494,602 (GRCm39) |
V870A |
probably benign |
Het |
| Cep192 |
A |
C |
18: 67,949,837 (GRCm39) |
Q307P |
probably benign |
Het |
| Cep63 |
T |
C |
9: 102,467,755 (GRCm39) |
|
probably benign |
Het |
| Cldn12 |
A |
G |
5: 5,558,385 (GRCm39) |
F14S |
probably damaging |
Het |
| Ctdsp1 |
G |
A |
1: 74,433,823 (GRCm39) |
V135I |
possibly damaging |
Het |
| Dcaf10 |
G |
A |
4: 45,372,769 (GRCm39) |
R394Q |
possibly damaging |
Het |
| Dchs1 |
T |
C |
7: 105,404,460 (GRCm39) |
D2694G |
probably damaging |
Het |
| Dchs1 |
C |
G |
7: 105,414,759 (GRCm39) |
G761A |
probably damaging |
Het |
| Dennd5b |
A |
G |
6: 148,946,277 (GRCm39) |
Y445H |
probably damaging |
Het |
| Dock1 |
T |
A |
7: 134,346,743 (GRCm39) |
L225* |
probably null |
Het |
| Drd3 |
G |
T |
16: 43,643,164 (GRCm39) |
E467* |
probably null |
Het |
| Dysf |
A |
T |
6: 84,074,738 (GRCm39) |
N527I |
probably damaging |
Het |
| Erbb2 |
A |
G |
11: 98,315,970 (GRCm39) |
T358A |
possibly damaging |
Het |
| Fhad1 |
A |
T |
4: 141,655,689 (GRCm39) |
|
probably null |
Het |
| Ganc |
T |
C |
2: 120,265,754 (GRCm39) |
I434T |
probably damaging |
Het |
| Gm5830 |
T |
A |
1: 78,945,549 (GRCm39) |
|
noncoding transcript |
Het |
| Gm6096 |
G |
T |
7: 33,950,484 (GRCm39) |
E8* |
probably null |
Het |
| Gne |
A |
G |
4: 44,066,806 (GRCm39) |
F63S |
probably benign |
Het |
| Gpat2 |
T |
C |
2: 127,273,902 (GRCm39) |
V315A |
possibly damaging |
Het |
| Gpr33 |
A |
G |
12: 52,070,892 (GRCm39) |
L49P |
probably damaging |
Het |
| Heatr1 |
C |
T |
13: 12,439,543 (GRCm39) |
Q1374* |
probably null |
Het |
| Hivep1 |
A |
G |
13: 42,316,887 (GRCm39) |
I2032V |
probably benign |
Het |
| Igkv2-112 |
A |
C |
6: 68,197,450 (GRCm39) |
I40L |
probably benign |
Het |
| Kcnab3 |
A |
G |
11: 69,221,294 (GRCm39) |
N204D |
probably benign |
Het |
| Kcnj10 |
T |
A |
1: 172,196,726 (GRCm39) |
F80Y |
probably damaging |
Het |
| Lcmt2 |
C |
G |
2: 120,969,911 (GRCm39) |
V171L |
probably benign |
Het |
| Loxhd1 |
T |
A |
18: 77,483,153 (GRCm39) |
Y1245N |
probably damaging |
Het |
| Lrrc7 |
GAAGTTGTTTGGAGATTCTTATCTTA |
GA |
3: 158,024,045 (GRCm39) |
|
probably benign |
Het |
| Mast1 |
A |
G |
8: 85,655,635 (GRCm39) |
S170P |
possibly damaging |
Het |
| Mroh4 |
A |
G |
15: 74,487,956 (GRCm39) |
L322P |
probably damaging |
Het |
| Nudcd3 |
A |
T |
11: 6,143,475 (GRCm39) |
V1D |
probably damaging |
Het |
| Pah |
T |
A |
10: 87,390,238 (GRCm39) |
L25Q |
probably damaging |
Het |
| Pik3cg |
A |
T |
12: 32,243,596 (GRCm39) |
|
probably null |
Het |
| Pira13 |
A |
C |
7: 3,824,547 (GRCm39) |
S611A |
probably benign |
Het |
| Plekha6 |
C |
A |
1: 133,211,058 (GRCm39) |
S625Y |
probably damaging |
Het |
| Rtn4 |
T |
A |
11: 29,658,362 (GRCm39) |
S839T |
probably damaging |
Het |
| Rusc1 |
A |
G |
3: 88,998,736 (GRCm39) |
S349P |
possibly damaging |
Het |
| Samsn1 |
A |
T |
16: 75,742,217 (GRCm39) |
|
noncoding transcript |
Het |
| Scimp |
A |
G |
11: 70,691,539 (GRCm39) |
V30A |
probably damaging |
Het |
| Serpinb13 |
C |
T |
1: 106,910,574 (GRCm39) |
S66L |
probably damaging |
Het |
| Sgip1 |
A |
G |
4: 102,823,419 (GRCm39) |
D680G |
probably damaging |
Het |
| Slc44a2 |
G |
A |
9: 21,259,691 (GRCm39) |
V613M |
probably damaging |
Het |
| Smpdl3b |
T |
C |
4: 132,472,489 (GRCm39) |
T95A |
probably damaging |
Het |
| Spag6l |
A |
T |
16: 16,610,395 (GRCm39) |
L85H |
probably damaging |
Het |
| Sucla2 |
T |
A |
14: 73,806,429 (GRCm39) |
Y167N |
possibly damaging |
Het |
| Svop |
G |
T |
5: 114,203,546 (GRCm39) |
|
probably benign |
Het |
| Tnxb |
A |
T |
17: 34,918,041 (GRCm39) |
D2318V |
probably damaging |
Het |
| Trbv14 |
A |
G |
6: 41,112,332 (GRCm39) |
D43G |
probably benign |
Het |
| Ubn2 |
A |
G |
6: 38,499,240 (GRCm39) |
|
probably benign |
Het |
| Ufsp1 |
T |
C |
5: 137,293,569 (GRCm39) |
I173T |
probably damaging |
Het |
| Zbtb40 |
A |
G |
4: 136,746,072 (GRCm39) |
|
probably benign |
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 |
|
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 |
|
R5605: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'- TGAAGTGGCCGCTTTTCTC -3'
(R):5'- TGGTCAAACAGTGGGTTGC -3'
Sequencing Primer
(F):5'- GTCCCTACCTGCTCGAAAC -3'
(R):5'- AAACAGTGGGTTGCGCACC -3'
|
| Posted On |
2015-11-11 |
Incidental Mutation