Incidental Mutation 'R5393:Npdc1'
ID |
425937 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Npdc1
|
Ensembl Gene |
ENSMUSG00000015094 |
Gene Name |
neural proliferation, differentiation and control 1 |
Synonyms |
NPDC-1 |
MMRRC Submission |
042965-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5393 (G1)
|
Quality Score |
211 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
25293062-25299506 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 25298682 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Leucine
at position 265
(M265L)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000071387
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055921]
[ENSMUST00000071442]
[ENSMUST00000133409]
[ENSMUST00000141567]
[ENSMUST00000154809]
|
AlphaFold |
Q64322 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000055921
AA Change: M274L
PolyPhen 2
Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000049602 Gene: ENSMUSG00000015094 AA Change: M274L
Domain | Start | End | E-Value | Type |
Pfam:NPDC1
|
1 |
341 |
9.1e-234 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000071442
AA Change: M265L
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000071387 Gene: ENSMUSG00000015094 AA Change: M265L
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 |
probably benign
Transcript: ENSMUST00000133409
AA Change: M207L
PolyPhen 2
Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000117773 Gene: ENSMUSG00000015094 AA Change: M207L
Domain | Start | End | E-Value | Type |
Pfam:NPDC1
|
1 |
274 |
3.4e-163 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136138
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141106
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144413
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156824
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000138651
|
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 |
0.4657 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
99% (72/73) |
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: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1110025L11Rik |
A |
T |
16: 88,860,653 (GRCm39) |
Y60* |
probably null |
Het |
Abca6 |
T |
A |
11: 110,135,121 (GRCm39) |
E221D |
probably benign |
Het |
Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
Adi1 |
A |
G |
12: 28,725,274 (GRCm39) |
D8G |
probably benign |
Het |
Adnp |
T |
C |
2: 168,024,869 (GRCm39) |
K809E |
possibly damaging |
Het |
Aldh18a1 |
T |
C |
19: 40,574,011 (GRCm39) |
H4R |
probably benign |
Het |
Atp6v0a1 |
T |
C |
11: 100,929,633 (GRCm39) |
S485P |
possibly damaging |
Het |
C1galt1 |
T |
C |
6: 7,864,143 (GRCm39) |
|
probably null |
Het |
Cacna2d4 |
A |
T |
6: 119,216,015 (GRCm39) |
N94I |
probably benign |
Het |
Catsperg1 |
T |
C |
7: 28,884,924 (GRCm39) |
N899S |
probably damaging |
Het |
Cilk1 |
A |
G |
9: 78,067,997 (GRCm39) |
T463A |
probably benign |
Het |
Coro2a |
A |
G |
4: 46,542,255 (GRCm39) |
S373P |
probably damaging |
Het |
Cpsf6 |
G |
C |
10: 117,197,921 (GRCm39) |
|
probably benign |
Het |
Csmd3 |
A |
T |
15: 47,497,099 (GRCm39) |
N3099K |
probably damaging |
Het |
Ctla2b |
T |
A |
13: 61,043,946 (GRCm39) |
E74D |
probably damaging |
Het |
Dnah2 |
T |
A |
11: 69,391,683 (GRCm39) |
T671S |
probably benign |
Het |
Drd5 |
T |
A |
5: 38,478,248 (GRCm39) |
S414T |
probably benign |
Het |
Dyrk2 |
C |
T |
10: 118,695,753 (GRCm39) |
D502N |
probably damaging |
Het |
Ecel1 |
A |
T |
1: 87,080,598 (GRCm39) |
L376Q |
possibly damaging |
Het |
Efcab8 |
G |
A |
2: 153,622,903 (GRCm39) |
R24Q |
unknown |
Het |
Eloc |
A |
C |
1: 16,718,192 (GRCm39) |
|
probably benign |
Het |
Ep300 |
A |
G |
15: 81,515,819 (GRCm39) |
|
probably benign |
Het |
Fam89b |
T |
C |
19: 5,778,733 (GRCm39) |
D152G |
probably damaging |
Het |
Gm15455 |
G |
A |
1: 33,875,927 (GRCm39) |
|
noncoding transcript |
Het |
Greb1l |
A |
G |
18: 10,458,312 (GRCm39) |
T30A |
probably benign |
Het |
Hdac10 |
T |
C |
15: 89,010,887 (GRCm39) |
Y238C |
probably damaging |
Het |
Ighv2-5 |
T |
C |
12: 113,649,502 (GRCm39) |
T12A |
possibly damaging |
Het |
Insrr |
T |
C |
3: 87,718,007 (GRCm39) |
|
probably null |
Het |
Irf9 |
T |
C |
14: 55,843,914 (GRCm39) |
|
probably benign |
Het |
Itpr2 |
A |
T |
6: 146,277,653 (GRCm39) |
C280* |
probably null |
Het |
Kcnk18 |
T |
C |
19: 59,208,271 (GRCm39) |
C36R |
probably damaging |
Het |
Khdc4 |
T |
A |
3: 88,603,913 (GRCm39) |
H243Q |
probably benign |
Het |
Klhl14 |
G |
T |
18: 21,785,051 (GRCm39) |
N125K |
probably benign |
Het |
Lce1i |
T |
C |
3: 92,685,042 (GRCm39) |
S45G |
unknown |
Het |
Lrmda |
A |
C |
14: 22,077,374 (GRCm39) |
D37A |
probably damaging |
Het |
Marco |
A |
C |
1: 120,413,583 (GRCm39) |
D280E |
probably damaging |
Het |
Meak7 |
T |
C |
8: 120,499,157 (GRCm39) |
I112V |
probably benign |
Het |
Miox |
C |
T |
15: 89,220,450 (GRCm39) |
Q180* |
probably null |
Het |
Nudcd3 |
T |
C |
11: 6,063,274 (GRCm39) |
K205R |
probably damaging |
Het |
Or2ak6 |
T |
A |
11: 58,593,326 (GRCm39) |
H266Q |
probably damaging |
Het |
Or2t46 |
C |
G |
11: 58,471,825 (GRCm39) |
L52V |
possibly damaging |
Het |
Pcdhga5 |
C |
T |
18: 37,829,720 (GRCm39) |
R723C |
probably benign |
Het |
Pdlim5 |
T |
A |
3: 141,964,947 (GRCm39) |
E295D |
probably damaging |
Het |
Poli |
C |
A |
18: 70,650,499 (GRCm39) |
E314* |
probably null |
Het |
Ptpro |
A |
G |
6: 137,357,222 (GRCm39) |
N238D |
probably benign |
Het |
R3hdm1 |
A |
G |
1: 128,159,084 (GRCm39) |
I920V |
probably benign |
Het |
Ralgapa2 |
C |
T |
2: 146,187,375 (GRCm39) |
V1338M |
probably damaging |
Het |
Saa3 |
T |
C |
7: 46,362,085 (GRCm39) |
Y53C |
probably damaging |
Het |
Septin14 |
T |
A |
5: 129,760,650 (GRCm39) |
E398D |
probably benign |
Het |
Six3 |
T |
C |
17: 85,931,270 (GRCm39) |
S309P |
possibly damaging |
Het |
Slc7a14 |
A |
G |
3: 31,311,919 (GRCm39) |
S34P |
probably damaging |
Het |
Smarca2 |
C |
A |
19: 26,617,829 (GRCm39) |
Q287K |
probably benign |
Het |
Stard9 |
C |
T |
2: 120,533,387 (GRCm39) |
L522F |
possibly damaging |
Het |
Sycp1 |
T |
C |
3: 102,748,363 (GRCm39) |
|
probably null |
Het |
Tbc1d8 |
A |
T |
1: 39,465,169 (GRCm39) |
V73E |
probably damaging |
Het |
Tmem120a |
T |
C |
5: 135,765,104 (GRCm39) |
|
probably null |
Het |
Tsc2 |
T |
C |
17: 24,819,370 (GRCm39) |
E1251G |
possibly damaging |
Het |
Vps51 |
T |
G |
19: 6,121,063 (GRCm39) |
E283D |
probably benign |
Het |
Wnt5b |
A |
C |
6: 119,417,394 (GRCm39) |
L157R |
probably damaging |
Het |
Zbtb24 |
T |
A |
10: 41,340,578 (GRCm39) |
V536E |
probably damaging |
Het |
Zfp593 |
G |
A |
4: 133,972,615 (GRCm39) |
A67V |
probably benign |
Het |
Zfp995 |
A |
T |
17: 22,099,473 (GRCm39) |
F254I |
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 |
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'- TCAGAAGGCTGACTATGCTG -3'
(R):5'- CAATGTATTGCTGCCCTGGG -3'
Sequencing Primer
(F):5'- CTGGAACTCACTTTGTAGACCAGG -3'
(R):5'- CCTGGGTAGGGGCCGTG -3'
|
Posted On |
2016-08-04 |