Incidental Mutation 'R5572:Npdc1'
| ID |
435704 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Npdc1
|
| Ensembl Gene |
ENSMUSG00000015094 |
| Gene Name |
neural proliferation, differentiation and control 1 |
| Synonyms |
NPDC-1 |
| MMRRC Submission |
043266-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5572 (G1)
|
| Quality Score |
208 |
|
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: 98.4%
- 20x: 95.2%
|
| Validation Efficiency |
100% (64/64) |
| 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 |
|---|
| Abcb1a |
C |
T |
5: 8,765,108 (GRCm39) |
|
probably null |
Het |
| Abcd4 |
T |
C |
12: 84,653,050 (GRCm39) |
D380G |
probably benign |
Het |
| Actr3b |
T |
A |
5: 26,014,886 (GRCm39) |
D68E |
probably benign |
Het |
| Apol10a |
T |
C |
15: 77,372,834 (GRCm39) |
S157P |
probably damaging |
Het |
| Arap3 |
A |
T |
18: 38,124,119 (GRCm39) |
I327N |
probably damaging |
Het |
| Arnt |
G |
T |
3: 95,382,015 (GRCm39) |
V198L |
possibly damaging |
Het |
| Baiap3 |
T |
A |
17: 25,470,449 (GRCm39) |
D86V |
possibly damaging |
Het |
| Bcl9l |
G |
T |
9: 44,412,095 (GRCm39) |
R27L |
possibly damaging |
Het |
| Bltp2 |
A |
T |
11: 78,155,393 (GRCm39) |
D167V |
probably damaging |
Het |
| C1qc |
T |
C |
4: 136,619,773 (GRCm39) |
Y34C |
probably benign |
Het |
| C1rb |
T |
C |
6: 124,557,758 (GRCm39) |
S632P |
probably benign |
Het |
| C3 |
A |
G |
17: 57,531,673 (GRCm39) |
S284P |
probably damaging |
Het |
| Cfap44 |
T |
G |
16: 44,301,668 (GRCm39) |
V1802G |
possibly damaging |
Het |
| Cfhr1 |
A |
G |
1: 139,484,165 (GRCm39) |
V117A |
possibly damaging |
Het |
| Clca3b |
T |
C |
3: 144,533,070 (GRCm39) |
D654G |
probably damaging |
Het |
| Col17a1 |
A |
T |
19: 47,639,168 (GRCm39) |
S1126T |
probably benign |
Het |
| Cts3 |
T |
A |
13: 61,712,782 (GRCm39) |
I313F |
probably damaging |
Het |
| Egfl7 |
T |
C |
2: 26,481,703 (GRCm39) |
V6A |
possibly damaging |
Het |
| Eif2s3y |
G |
A |
Y: 1,016,631 (GRCm39) |
D272N |
probably damaging |
Het |
| Foxp4 |
A |
G |
17: 48,191,804 (GRCm39) |
V111A |
unknown |
Het |
| Hmcn2 |
A |
T |
2: 31,304,537 (GRCm39) |
|
probably null |
Het |
| Hmcn2 |
G |
A |
2: 31,304,538 (GRCm39) |
|
probably null |
Het |
| Igsf11 |
C |
T |
16: 38,845,294 (GRCm39) |
R283C |
probably damaging |
Het |
| Il1a |
A |
G |
2: 129,149,838 (GRCm39) |
Y21H |
possibly damaging |
Het |
| Il6ra |
A |
T |
3: 89,778,589 (GRCm39) |
V420D |
probably damaging |
Het |
| Kdm5a |
T |
C |
6: 120,389,336 (GRCm39) |
V921A |
possibly damaging |
Het |
| Kirrel3 |
G |
A |
9: 34,912,244 (GRCm39) |
A196T |
probably damaging |
Het |
| Klra1 |
T |
A |
6: 130,349,802 (GRCm39) |
D212V |
possibly damaging |
Het |
| N4bp2l2 |
G |
A |
5: 150,585,755 (GRCm39) |
T75I |
probably benign |
Het |
| Niban1 |
T |
C |
1: 151,584,941 (GRCm39) |
S513P |
probably benign |
Het |
| Nnmt |
A |
G |
9: 48,503,447 (GRCm39) |
L193P |
probably damaging |
Het |
| Ntm |
A |
G |
9: 28,925,512 (GRCm39) |
I191T |
probably damaging |
Het |
| Or2ak5 |
A |
G |
11: 58,611,055 (GRCm39) |
V273A |
probably benign |
Het |
| Or52d13 |
A |
C |
7: 103,109,905 (GRCm39) |
L170R |
probably benign |
Het |
| Or52h7 |
A |
T |
7: 104,214,201 (GRCm39) |
T258S |
probably benign |
Het |
| Pam |
A |
C |
1: 97,782,469 (GRCm39) |
|
probably benign |
Het |
| Pomk |
T |
A |
8: 26,473,218 (GRCm39) |
H245L |
possibly damaging |
Het |
| Rapgef4 |
G |
A |
2: 71,864,464 (GRCm39) |
|
probably null |
Het |
| Rasip1 |
G |
T |
7: 45,286,153 (GRCm39) |
R792L |
probably benign |
Het |
| Ret |
T |
C |
6: 118,132,392 (GRCm39) |
Y1016C |
probably damaging |
Het |
| Rhbdd1 |
A |
T |
1: 82,318,531 (GRCm39) |
N138I |
possibly damaging |
Het |
| Snx13 |
T |
G |
12: 35,153,119 (GRCm39) |
V383G |
probably damaging |
Het |
| Syt3 |
A |
G |
7: 44,040,142 (GRCm39) |
H125R |
probably benign |
Het |
| Tlr6 |
A |
T |
5: 65,112,361 (GRCm39) |
L182Q |
probably damaging |
Het |
| Tlr9 |
T |
C |
9: 106,102,836 (GRCm39) |
V709A |
possibly damaging |
Het |
| Tmprss6 |
T |
C |
15: 78,326,622 (GRCm39) |
Y655C |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,683,972 (GRCm39) |
|
probably benign |
Het |
| Ube3a |
T |
C |
7: 58,938,525 (GRCm39) |
I761T |
probably damaging |
Het |
| Ube3b |
G |
A |
5: 114,544,240 (GRCm39) |
D546N |
probably damaging |
Het |
| Ugt2b36 |
A |
G |
5: 87,237,341 (GRCm39) |
V188A |
possibly damaging |
Het |
| Usp29 |
A |
G |
7: 6,965,191 (GRCm39) |
I345V |
probably benign |
Het |
| Vmn2r78 |
A |
G |
7: 86,564,720 (GRCm39) |
K55R |
probably benign |
Het |
| Wdsub1 |
A |
G |
2: 59,693,051 (GRCm39) |
F288L |
possibly damaging |
Het |
| Zan |
C |
T |
5: 137,392,693 (GRCm39) |
V4601M |
unknown |
Het |
| Zbtb8b |
T |
C |
4: 129,322,334 (GRCm39) |
K376E |
probably damaging |
Het |
| Zfp619 |
A |
T |
7: 39,184,663 (GRCm39) |
Y231F |
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 |
|
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 |
|
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'- TGAAGTGGCCGCTTTTCTCC -3'
(R):5'- TCAAACAGTGGGTTGCGCAC -3'
Sequencing Primer
(F):5'- GTCCCTACCTGCTCGAAAC -3'
(R):5'- TGGGTTGCGCACCTCCATC -3'
|
| Posted On |
2016-10-24 |
Incidental Mutation