Incidental Mutation 'R6215:Npc1'
| ID |
503681 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Npc1
|
| Ensembl Gene |
ENSMUSG00000024413 |
| Gene Name |
NPC intracellular cholesterol transporter 1 |
| Synonyms |
lcsd, nmf164, D18Ertd139e, D18Ertd723e, A430089E03Rik, C85354 |
| MMRRC Submission |
044348-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.616)
|
| Stock # |
R6215 (G1)
|
| Quality Score |
108.467 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
12322749-12369457 bp(-) (GRCm39) |
| Type of Mutation |
small deletion (1 aa in frame mutation) |
| DNA Base Change (assembly) |
ACAGCAGCAGCAGCAGCAG to ACAGCAGCAGCAGCAG
at 12369249 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000025279
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025279]
|
| AlphaFold |
O35604 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025279
|
| SMART Domains |
Protein: ENSMUSP00000025279
Gene: ENSMUSG00000024413
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
8 |
15 |
N/A |
INTRINSIC |
|
Pfam:NPC1_N
|
22 |
267 |
1.6e-79 |
PFAM |
|
transmembrane domain
|
269 |
291 |
N/A |
INTRINSIC |
|
transmembrane domain
|
353 |
375 |
N/A |
INTRINSIC |
|
Pfam:Patched
|
436 |
896 |
3.5e-52 |
PFAM |
|
Pfam:MMPL
|
648 |
794 |
6.3e-8 |
PFAM |
|
Pfam:Sterol-sensing
|
649 |
803 |
2.7e-56 |
PFAM |
|
Pfam:Patched
|
1023 |
1252 |
2.9e-33 |
PFAM |
|
low complexity region
|
1259 |
1273 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000133112
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149211
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
| Validation Efficiency |
95% (42/44) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.[provided by RefSeq, Aug 2009]
PHENOTYPE: Homozygotes for spontaneous and chemically induced mutations may exhibit lysosomal storage of non-esterified cholesterol, neurodegeneration, ataxia, presence of foam cells, sterility, and shortened lifespan. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrv1 |
C |
T |
13: 81,727,713 (GRCm39) |
W309* |
probably null |
Het |
| Aox1 |
G |
A |
1: 58,124,620 (GRCm39) |
V954I |
probably benign |
Het |
| Asnsd1 |
A |
C |
1: 53,387,187 (GRCm39) |
|
probably null |
Het |
| Aste1 |
A |
G |
9: 105,274,056 (GRCm39) |
K38E |
probably damaging |
Het |
| Catsperg1 |
A |
G |
7: 28,899,664 (GRCm39) |
V339A |
probably damaging |
Het |
| Ccdc13 |
A |
G |
9: 121,627,975 (GRCm39) |
|
probably benign |
Het |
| Cd79b |
C |
A |
11: 106,203,267 (GRCm39) |
|
probably null |
Het |
| Cemip2 |
C |
A |
19: 21,789,751 (GRCm39) |
N650K |
probably benign |
Het |
| Chd3 |
A |
G |
11: 69,247,380 (GRCm39) |
L981P |
probably damaging |
Het |
| Chia1 |
T |
C |
3: 106,029,761 (GRCm39) |
F132L |
probably damaging |
Het |
| Dhx9 |
G |
A |
1: 153,348,209 (GRCm39) |
P336S |
probably damaging |
Het |
| Dido1 |
T |
C |
2: 180,303,945 (GRCm39) |
K1320E |
probably damaging |
Het |
| Dmbt1 |
G |
T |
7: 130,668,463 (GRCm39) |
C573F |
possibly damaging |
Het |
| Dmtn |
A |
G |
14: 70,850,776 (GRCm39) |
I205T |
probably benign |
Het |
| Efnb3 |
C |
A |
11: 69,447,591 (GRCm39) |
V181L |
probably benign |
Het |
| Flg2 |
G |
T |
3: 93,109,166 (GRCm39) |
C398F |
possibly damaging |
Het |
| Gabbr1 |
A |
G |
17: 37,380,257 (GRCm39) |
D604G |
probably damaging |
Het |
| Glis2 |
T |
A |
16: 4,428,197 (GRCm39) |
L83* |
probably null |
Het |
| Gm10719 |
T |
A |
9: 3,019,040 (GRCm39) |
|
probably null |
Homo |
| Hipk3 |
T |
C |
2: 104,264,086 (GRCm39) |
D804G |
probably damaging |
Het |
| Kcnd1 |
G |
C |
X: 7,690,148 (GRCm39) |
A23P |
probably damaging |
Homo |
| Kcnj13 |
A |
G |
1: 87,314,256 (GRCm39) |
V322A |
probably benign |
Het |
| Nav3 |
A |
G |
10: 109,688,426 (GRCm39) |
L617P |
probably damaging |
Het |
| Or8b3b |
A |
G |
9: 38,584,510 (GRCm39) |
S90P |
probably benign |
Het |
| Osgin1 |
G |
A |
8: 120,172,183 (GRCm39) |
V326I |
probably benign |
Het |
| Pcsk7 |
A |
C |
9: 45,821,674 (GRCm39) |
N156T |
possibly damaging |
Het |
| Pde4d |
C |
T |
13: 110,085,967 (GRCm39) |
S515L |
probably damaging |
Het |
| Peg10 |
GC |
GCCCC |
6: 4,756,452 (GRCm39) |
|
probably benign |
Het |
| Ppp2r5a |
T |
A |
1: 191,094,447 (GRCm39) |
Q191L |
probably benign |
Het |
| Prom2 |
A |
G |
2: 127,381,695 (GRCm39) |
|
probably null |
Het |
| Rsf1 |
CG |
CGACGGCGGTG |
7: 97,229,115 (GRCm39) |
|
probably benign |
Het |
| Sart3 |
C |
T |
5: 113,881,267 (GRCm39) |
A938T |
probably benign |
Het |
| Scn3a |
T |
C |
2: 65,325,380 (GRCm39) |
I1046V |
probably benign |
Het |
| Sh3glb2 |
T |
C |
2: 30,235,805 (GRCm39) |
E313G |
possibly damaging |
Het |
| Slc13a1 |
A |
T |
6: 24,090,795 (GRCm39) |
Y541* |
probably null |
Het |
| Smtnl2 |
G |
A |
11: 72,292,225 (GRCm39) |
A274V |
probably damaging |
Het |
| Spata31h1 |
T |
A |
10: 82,126,946 (GRCm39) |
K2021N |
probably benign |
Het |
| Speer1d |
C |
T |
5: 11,307,197 (GRCm39) |
T25I |
probably damaging |
Het |
| Tm6sf2 |
T |
C |
8: 70,525,724 (GRCm39) |
V27A |
possibly damaging |
Het |
| Tmem116 |
C |
T |
5: 121,629,171 (GRCm39) |
T188M |
probably benign |
Het |
| Trim21 |
A |
G |
7: 102,208,646 (GRCm39) |
S358P |
probably damaging |
Het |
| Ttc21a |
A |
G |
9: 119,795,838 (GRCm39) |
Y1224C |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,710,552 (GRCm39) |
|
probably benign |
Het |
| Vmn2r99 |
A |
G |
17: 19,602,820 (GRCm39) |
Q525R |
probably benign |
Het |
|
| Other mutations in Npc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02347:Npc1
|
APN |
18 |
12,332,691 (GRCm39) |
missense |
probably benign |
0.45 |
|
IGL02523:Npc1
|
APN |
18 |
12,334,629 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03018:Npc1
|
APN |
18 |
12,347,436 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03101:Npc1
|
APN |
18 |
12,331,596 (GRCm39) |
missense |
probably benign |
0.15 |
|
IGL03151:Npc1
|
APN |
18 |
12,352,332 (GRCm39) |
missense |
probably benign |
0.05 |
|
IGL03377:Npc1
|
APN |
18 |
12,344,878 (GRCm39) |
missense |
probably benign |
|
|
PIT4354001:Npc1
|
UTSW |
18 |
12,344,592 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0068:Npc1
|
UTSW |
18 |
12,341,424 (GRCm39) |
missense |
probably benign |
0.04 |
|
R0068:Npc1
|
UTSW |
18 |
12,341,424 (GRCm39) |
missense |
probably benign |
0.04 |
|
R0190:Npc1
|
UTSW |
18 |
12,324,887 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0200:Npc1
|
UTSW |
18 |
12,352,261 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0485:Npc1
|
UTSW |
18 |
12,346,503 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0699:Npc1
|
UTSW |
18 |
12,343,632 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0730:Npc1
|
UTSW |
18 |
12,352,382 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1302:Npc1
|
UTSW |
18 |
12,328,142 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1442:Npc1
|
UTSW |
18 |
12,328,106 (GRCm39) |
missense |
probably benign |
|
|
R1463:Npc1
|
UTSW |
18 |
12,324,887 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1804:Npc1
|
UTSW |
18 |
12,356,145 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1808:Npc1
|
UTSW |
18 |
12,327,149 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1928:Npc1
|
UTSW |
18 |
12,346,435 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R2112:Npc1
|
UTSW |
18 |
12,346,529 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R2117:Npc1
|
UTSW |
18 |
12,329,613 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2157:Npc1
|
UTSW |
18 |
12,324,866 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2279:Npc1
|
UTSW |
18 |
12,330,236 (GRCm39) |
splice site |
probably null |
|
|
R2311:Npc1
|
UTSW |
18 |
12,335,240 (GRCm39) |
missense |
probably benign |
|
|
R2446:Npc1
|
UTSW |
18 |
12,347,396 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3004:Npc1
|
UTSW |
18 |
12,330,311 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4090:Npc1
|
UTSW |
18 |
12,331,219 (GRCm39) |
splice site |
probably null |
|
|
R4304:Npc1
|
UTSW |
18 |
12,343,584 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R4308:Npc1
|
UTSW |
18 |
12,343,584 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R4564:Npc1
|
UTSW |
18 |
12,324,789 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4786:Npc1
|
UTSW |
18 |
12,332,554 (GRCm39) |
missense |
probably benign |
0.35 |
|
R5243:Npc1
|
UTSW |
18 |
12,331,688 (GRCm39) |
intron |
probably benign |
|
|
R5404:Npc1
|
UTSW |
18 |
12,346,356 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R5823:Npc1
|
UTSW |
18 |
12,324,846 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6080:Npc1
|
UTSW |
18 |
12,352,408 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6301:Npc1
|
UTSW |
18 |
12,330,302 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6476:Npc1
|
UTSW |
18 |
12,334,751 (GRCm39) |
nonsense |
probably null |
|
|
R7007:Npc1
|
UTSW |
18 |
12,343,605 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7020:Npc1
|
UTSW |
18 |
12,331,594 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7048:Npc1
|
UTSW |
18 |
12,337,822 (GRCm39) |
splice site |
probably null |
|
|
R7116:Npc1
|
UTSW |
18 |
12,344,601 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7153:Npc1
|
UTSW |
18 |
12,346,348 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
R7359:Npc1
|
UTSW |
18 |
12,328,237 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7382:Npc1
|
UTSW |
18 |
12,334,763 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7765:Npc1
|
UTSW |
18 |
12,328,105 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8047:Npc1
|
UTSW |
18 |
12,346,374 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8094:Npc1
|
UTSW |
18 |
12,327,297 (GRCm39) |
missense |
probably benign |
|
|
R8161:Npc1
|
UTSW |
18 |
12,328,129 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R8310:Npc1
|
UTSW |
18 |
12,326,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8821:Npc1
|
UTSW |
18 |
12,333,877 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8831:Npc1
|
UTSW |
18 |
12,333,877 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8847:Npc1
|
UTSW |
18 |
12,323,987 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9022:Npc1
|
UTSW |
18 |
12,346,422 (GRCm39) |
missense |
probably benign |
|
|
R9343:Npc1
|
UTSW |
18 |
12,334,769 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R9460:Npc1
|
UTSW |
18 |
12,346,398 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R9723:Npc1
|
UTSW |
18 |
12,343,649 (GRCm39) |
missense |
probably benign |
|
|
X0012:Npc1
|
UTSW |
18 |
12,326,368 (GRCm39) |
splice site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ATAGAGGCCCCTAGCTGTCATC -3'
(R):5'- AACCTGCATCTAAGGCACG -3'
Sequencing Primer
(F):5'- AGCTGTCATCCTCTCCCAGAG -3'
(R):5'- AATGCGCTCTAAGCCGG -3'
|
| Posted On |
2018-02-27 |
Incidental Mutation