Incidental Mutation 'IGL01773:Sptlc1'
| ID |
153735 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Sptlc1
|
| Ensembl Gene |
ENSMUSG00000021468 |
| Gene Name |
serine palmitoyltransferase, long chain base subunit 1 |
| Synonyms |
Spt1, Lcb1 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01773
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
13 |
| Chromosomal Location |
53486784-53531433 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 53531334 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 18
(Y18H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021920
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021920]
|
| AlphaFold |
O35704 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021920
AA Change: Y18H
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: Y18H
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
20 |
40 |
N/A |
INTRINSIC |
|
Pfam:Aminotran_1_2
|
98 |
464 |
9.5e-44 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000221265
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000221709
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a knock-out allele exhibit abnormal sphingolipid levels. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Cacna1s |
C |
A |
1: 136,046,491 (GRCm39) |
H1775Q |
probably benign |
Het |
| Calcrl |
A |
G |
2: 84,200,787 (GRCm39) |
Y86H |
probably benign |
Het |
| Ccdc63 |
T |
C |
5: 122,251,208 (GRCm39) |
K401E |
possibly damaging |
Het |
| Col9a1 |
A |
G |
1: 24,244,147 (GRCm39) |
T127A |
probably benign |
Het |
| Cpq |
T |
A |
15: 33,212,996 (GRCm39) |
F5Y |
probably benign |
Het |
| Cuzd1 |
T |
A |
7: 130,916,614 (GRCm39) |
M282L |
probably damaging |
Het |
| Ddx10 |
C |
A |
9: 53,115,430 (GRCm39) |
D635Y |
possibly damaging |
Het |
| Ect2l |
T |
C |
10: 18,037,252 (GRCm39) |
D382G |
probably damaging |
Het |
| Ganc |
T |
C |
2: 120,290,365 (GRCm39) |
S901P |
possibly damaging |
Het |
| Gpr179 |
G |
A |
11: 97,232,192 (GRCm39) |
R671C |
probably benign |
Het |
| Isl2 |
T |
C |
9: 55,451,504 (GRCm39) |
L219P |
probably damaging |
Het |
| Mfsd13a |
T |
C |
19: 46,357,733 (GRCm39) |
S296P |
possibly damaging |
Het |
| Mtmr7 |
A |
T |
8: 41,034,461 (GRCm39) |
L287Q |
probably damaging |
Het |
| Or11g25 |
T |
C |
14: 50,723,230 (GRCm39) |
F105S |
probably damaging |
Het |
| Or52d13 |
T |
G |
7: 103,110,221 (GRCm39) |
M60L |
possibly damaging |
Het |
| Or7a39 |
A |
G |
10: 78,715,770 (GRCm39) |
T255A |
possibly damaging |
Het |
| Or8g28 |
A |
G |
9: 39,169,830 (GRCm39) |
I46T |
probably damaging |
Het |
| Pik3c3 |
T |
A |
18: 30,410,155 (GRCm39) |
F130I |
probably damaging |
Het |
| Rab3gap1 |
T |
A |
1: 127,845,958 (GRCm39) |
S277R |
possibly damaging |
Het |
| Rassf9 |
A |
G |
10: 102,381,494 (GRCm39) |
K290R |
probably benign |
Het |
| Rnaseh2a |
A |
T |
8: 85,691,767 (GRCm39) |
V136D |
probably damaging |
Het |
| Rnf39 |
C |
T |
17: 37,256,328 (GRCm39) |
S140L |
possibly damaging |
Het |
| Sbno2 |
A |
G |
10: 79,893,665 (GRCm39) |
V1212A |
probably damaging |
Het |
| Slc4a10 |
A |
T |
2: 62,021,101 (GRCm39) |
I50F |
probably damaging |
Het |
| Slfn5 |
A |
T |
11: 82,852,157 (GRCm39) |
E761V |
probably damaging |
Het |
| Tfam |
A |
G |
10: 71,072,805 (GRCm39) |
M9T |
possibly damaging |
Het |
| Tmem186 |
A |
G |
16: 8,453,841 (GRCm39) |
L140P |
probably damaging |
Het |
| Try4 |
A |
T |
6: 41,281,960 (GRCm39) |
N182I |
probably damaging |
Het |
| Vmn1r209 |
C |
T |
13: 22,990,450 (GRCm39) |
C80Y |
probably damaging |
Het |
| Vmn2r104 |
A |
T |
17: 20,260,930 (GRCm39) |
S498T |
probably benign |
Het |
|
| Other mutations in Sptlc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00811:Sptlc1
|
APN |
13 |
53,521,414 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL01354:Sptlc1
|
APN |
13 |
53,487,987 (GRCm39) |
missense |
probably benign |
|
|
IGL01876:Sptlc1
|
APN |
13 |
53,528,048 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0390:Sptlc1
|
UTSW |
13 |
53,491,648 (GRCm39) |
missense |
probably benign |
0.06 |
|
R1371:Sptlc1
|
UTSW |
13 |
53,505,660 (GRCm39) |
missense |
probably benign |
|
|
R1961:Sptlc1
|
UTSW |
13 |
53,512,916 (GRCm39) |
missense |
probably benign |
|
|
R2179:Sptlc1
|
UTSW |
13 |
53,505,675 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2513:Sptlc1
|
UTSW |
13 |
53,491,676 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R4357:Sptlc1
|
UTSW |
13 |
53,528,068 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4989:Sptlc1
|
UTSW |
13 |
53,505,692 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5055:Sptlc1
|
UTSW |
13 |
53,496,218 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6415:Sptlc1
|
UTSW |
13 |
53,505,728 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R6752:Sptlc1
|
UTSW |
13 |
53,489,394 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R7283:Sptlc1
|
UTSW |
13 |
53,498,914 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7548:Sptlc1
|
UTSW |
13 |
53,521,968 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R7731:Sptlc1
|
UTSW |
13 |
53,487,993 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9268:Sptlc1
|
UTSW |
13 |
53,512,872 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9302:Sptlc1
|
UTSW |
13 |
53,528,047 (GRCm39) |
missense |
probably benign |
0.06 |
|
R9794:Sptlc1
|
UTSW |
13 |
53,512,803 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
| Posted On |
2014-02-04 |
Incidental Mutation