Incidental Mutation 'R5162:Sptlc3'
ID |
397036 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sptlc3
|
Ensembl Gene |
ENSMUSG00000039092 |
Gene Name |
serine palmitoyltransferase, long chain base subunit 3 |
Synonyms |
C130053K05Rik |
MMRRC Submission |
042744-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.122)
|
Stock # |
R5162 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 139473263 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Lysine
at position 504
(M504K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000105710
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047370]
[ENSMUST00000110083]
|
AlphaFold |
Q8BG54 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000047370
AA Change: M504K
PolyPhen 2
Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)
|
SMART Domains |
Protein: ENSMUSP00000048313 Gene: ENSMUSG00000039092 AA Change: M504K
Domain | Start | End | E-Value | Type |
transmembrane domain
|
60 |
79 |
N/A |
INTRINSIC |
Pfam:Aminotran_1_2
|
160 |
520 |
4.8e-59 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000110083
AA Change: M504K
PolyPhen 2
Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)
|
SMART Domains |
Protein: ENSMUSP00000105710 Gene: ENSMUSG00000039092 AA Change: M504K
Domain | Start | End | E-Value | Type |
transmembrane domain
|
60 |
79 |
N/A |
INTRINSIC |
Pfam:Aminotran_1_2
|
160 |
520 |
4.8e-59 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000134801
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
Validation Efficiency |
98% (61/62) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
2010315B03Rik |
T |
A |
9: 124,056,301 (GRCm39) |
T229S |
probably benign |
Het |
Adrb3 |
T |
C |
8: 27,717,348 (GRCm39) |
E367G |
probably benign |
Het |
Ak9 |
T |
A |
10: 41,233,653 (GRCm39) |
N630K |
probably damaging |
Het |
Atp8b1 |
T |
C |
18: 64,694,733 (GRCm39) |
I516M |
possibly damaging |
Het |
Bcor |
C |
T |
X: 11,906,725 (GRCm39) |
R1551Q |
probably damaging |
Het |
Cry1 |
T |
A |
10: 84,969,150 (GRCm39) |
H558L |
probably benign |
Het |
Cstdc3 |
A |
T |
16: 36,132,918 (GRCm39) |
H65L |
probably damaging |
Het |
Cyp3a57 |
T |
A |
5: 145,305,893 (GRCm39) |
W126R |
probably damaging |
Het |
Dhx36 |
A |
T |
3: 62,401,201 (GRCm39) |
V355E |
probably damaging |
Het |
Dpp6 |
A |
G |
5: 27,604,013 (GRCm39) |
|
probably benign |
Het |
Ehmt1 |
G |
T |
2: 24,767,509 (GRCm39) |
P135T |
probably damaging |
Het |
Enpp2 |
T |
C |
15: 54,710,692 (GRCm39) |
D694G |
probably benign |
Het |
Esrp2 |
T |
C |
8: 106,859,930 (GRCm39) |
E336G |
probably damaging |
Het |
Faah |
A |
T |
4: 115,857,938 (GRCm39) |
|
probably benign |
Het |
Fat1 |
G |
A |
8: 45,478,846 (GRCm39) |
G2608R |
probably benign |
Het |
Fbxo8 |
A |
T |
8: 57,022,354 (GRCm39) |
Y122F |
probably damaging |
Het |
Fgd5 |
A |
G |
6: 92,051,215 (GRCm39) |
D1497G |
probably damaging |
Het |
Fn3krp |
T |
C |
11: 121,320,410 (GRCm39) |
F252L |
probably damaging |
Het |
Fnip2 |
T |
C |
3: 79,389,084 (GRCm39) |
Y549C |
probably damaging |
Het |
Gcm2 |
T |
C |
13: 41,257,131 (GRCm39) |
N206S |
probably benign |
Het |
Grn |
C |
A |
11: 102,321,380 (GRCm39) |
|
probably benign |
Het |
H2-T10 |
T |
A |
17: 36,429,843 (GRCm39) |
|
probably null |
Het |
Henmt1 |
T |
C |
3: 108,847,366 (GRCm39) |
|
probably null |
Het |
Man1b1 |
T |
A |
2: 25,233,365 (GRCm39) |
L246Q |
probably damaging |
Het |
Mdh2 |
T |
C |
5: 135,812,329 (GRCm39) |
|
probably null |
Het |
Mocos |
T |
C |
18: 24,787,109 (GRCm39) |
F43L |
probably damaging |
Het |
Msh2 |
C |
A |
17: 88,030,841 (GRCm39) |
A906E |
probably benign |
Het |
Naip5 |
T |
A |
13: 100,359,914 (GRCm39) |
I441F |
possibly damaging |
Het |
Naip6 |
C |
T |
13: 100,437,108 (GRCm39) |
A472T |
probably benign |
Het |
Nars2 |
T |
C |
7: 96,709,027 (GRCm39) |
|
probably benign |
Het |
Ncoa2 |
A |
T |
1: 13,245,396 (GRCm39) |
M434K |
possibly damaging |
Het |
Nlrp4g |
T |
A |
9: 124,350,394 (GRCm38) |
|
noncoding transcript |
Het |
Or14j8 |
T |
A |
17: 38,263,255 (GRCm39) |
Q220L |
probably benign |
Het |
Or9a2 |
G |
T |
6: 41,748,706 (GRCm39) |
H176N |
possibly damaging |
Het |
Pals2 |
T |
A |
6: 50,155,495 (GRCm39) |
W259R |
probably damaging |
Het |
Pars2 |
A |
G |
4: 106,511,735 (GRCm39) |
T506A |
probably benign |
Het |
Pkp2 |
T |
C |
16: 16,078,200 (GRCm39) |
S481P |
probably damaging |
Het |
Plod3 |
T |
C |
5: 137,020,161 (GRCm39) |
W459R |
probably damaging |
Het |
Pramel13 |
A |
T |
4: 144,121,482 (GRCm39) |
L181M |
probably damaging |
Het |
Prdm10 |
A |
T |
9: 31,251,714 (GRCm39) |
I361F |
possibly damaging |
Het |
Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
Raver2 |
T |
C |
4: 100,959,921 (GRCm39) |
C134R |
probably damaging |
Het |
Rnf130 |
G |
C |
11: 49,943,722 (GRCm39) |
A123P |
probably damaging |
Het |
Slc29a4 |
G |
A |
5: 142,707,207 (GRCm39) |
A517T |
possibly damaging |
Het |
Slc38a6 |
T |
A |
12: 73,376,759 (GRCm39) |
S138T |
possibly damaging |
Het |
Spred1 |
T |
C |
2: 117,008,102 (GRCm39) |
V336A |
possibly damaging |
Het |
Syt11 |
T |
C |
3: 88,655,149 (GRCm39) |
D78G |
probably damaging |
Het |
Trim23 |
C |
T |
13: 104,317,682 (GRCm39) |
T61I |
probably damaging |
Het |
Tsg101 |
T |
C |
7: 46,542,174 (GRCm39) |
T260A |
probably damaging |
Het |
Tyw5 |
T |
C |
1: 57,440,618 (GRCm39) |
Y48C |
probably damaging |
Het |
Utp25 |
G |
T |
1: 192,796,089 (GRCm39) |
T192K |
probably damaging |
Het |
Vmn1r17 |
A |
G |
6: 57,337,828 (GRCm39) |
V130A |
probably benign |
Het |
Vmn2r89 |
C |
A |
14: 51,693,620 (GRCm39) |
H323Q |
possibly damaging |
Het |
Vps18 |
A |
G |
2: 119,123,423 (GRCm39) |
S117G |
probably benign |
Het |
Zfp93 |
C |
G |
7: 23,975,757 (GRCm39) |
Q581E |
probably damaging |
Het |
|
Other mutations in Sptlc3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01392:Sptlc3
|
APN |
2 |
139,388,341 (GRCm39) |
missense |
possibly damaging |
0.55 |
IGL01537:Sptlc3
|
APN |
2 |
139,431,615 (GRCm39) |
missense |
possibly damaging |
0.95 |
IGL01996:Sptlc3
|
APN |
2 |
139,423,424 (GRCm39) |
splice site |
probably benign |
|
IGL02512:Sptlc3
|
APN |
2 |
139,389,123 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03278:Sptlc3
|
APN |
2 |
139,431,579 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03286:Sptlc3
|
APN |
2 |
139,431,579 (GRCm39) |
missense |
probably damaging |
1.00 |
R0266:Sptlc3
|
UTSW |
2 |
139,437,957 (GRCm39) |
missense |
possibly damaging |
0.93 |
R0362:Sptlc3
|
UTSW |
2 |
139,388,475 (GRCm39) |
splice site |
probably benign |
|
R1464:Sptlc3
|
UTSW |
2 |
139,389,154 (GRCm39) |
missense |
probably benign |
0.00 |
R1464:Sptlc3
|
UTSW |
2 |
139,389,154 (GRCm39) |
missense |
probably benign |
0.00 |
R1494:Sptlc3
|
UTSW |
2 |
139,431,480 (GRCm39) |
missense |
possibly damaging |
0.58 |
R1847:Sptlc3
|
UTSW |
2 |
139,467,843 (GRCm39) |
missense |
probably benign |
0.08 |
R1919:Sptlc3
|
UTSW |
2 |
139,408,595 (GRCm39) |
missense |
possibly damaging |
0.66 |
R2093:Sptlc3
|
UTSW |
2 |
139,467,794 (GRCm39) |
missense |
possibly damaging |
0.89 |
R2396:Sptlc3
|
UTSW |
2 |
139,408,506 (GRCm39) |
missense |
probably benign |
0.44 |
R2972:Sptlc3
|
UTSW |
2 |
139,431,581 (GRCm39) |
missense |
probably damaging |
1.00 |
R2973:Sptlc3
|
UTSW |
2 |
139,431,581 (GRCm39) |
missense |
probably damaging |
1.00 |
R2974:Sptlc3
|
UTSW |
2 |
139,431,581 (GRCm39) |
missense |
probably damaging |
1.00 |
R4601:Sptlc3
|
UTSW |
2 |
139,478,600 (GRCm39) |
missense |
probably benign |
0.01 |
R4602:Sptlc3
|
UTSW |
2 |
139,478,600 (GRCm39) |
missense |
probably benign |
0.01 |
R4610:Sptlc3
|
UTSW |
2 |
139,478,600 (GRCm39) |
missense |
probably benign |
0.01 |
R4745:Sptlc3
|
UTSW |
2 |
139,389,087 (GRCm39) |
missense |
probably damaging |
1.00 |
R4779:Sptlc3
|
UTSW |
2 |
139,431,509 (GRCm39) |
missense |
probably benign |
0.04 |
R4992:Sptlc3
|
UTSW |
2 |
139,437,923 (GRCm39) |
missense |
probably benign |
0.04 |
R5401:Sptlc3
|
UTSW |
2 |
139,478,643 (GRCm39) |
missense |
possibly damaging |
0.75 |
R5406:Sptlc3
|
UTSW |
2 |
139,388,398 (GRCm39) |
missense |
probably benign |
0.26 |
R5642:Sptlc3
|
UTSW |
2 |
139,388,328 (GRCm39) |
missense |
probably damaging |
0.96 |
R5840:Sptlc3
|
UTSW |
2 |
139,389,126 (GRCm39) |
missense |
probably damaging |
1.00 |
R6057:Sptlc3
|
UTSW |
2 |
139,423,533 (GRCm39) |
missense |
probably damaging |
0.99 |
R6376:Sptlc3
|
UTSW |
2 |
139,478,692 (GRCm39) |
missense |
probably benign |
0.21 |
R6852:Sptlc3
|
UTSW |
2 |
139,408,506 (GRCm39) |
missense |
probably benign |
0.44 |
R7026:Sptlc3
|
UTSW |
2 |
139,379,608 (GRCm39) |
missense |
probably benign |
|
R7412:Sptlc3
|
UTSW |
2 |
139,431,537 (GRCm39) |
missense |
possibly damaging |
0.75 |
R7516:Sptlc3
|
UTSW |
2 |
139,431,438 (GRCm39) |
missense |
probably benign |
0.11 |
R7733:Sptlc3
|
UTSW |
2 |
139,473,288 (GRCm39) |
missense |
possibly damaging |
0.77 |
R7826:Sptlc3
|
UTSW |
2 |
139,389,115 (GRCm39) |
missense |
probably benign |
0.44 |
R7949:Sptlc3
|
UTSW |
2 |
139,467,795 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9224:Sptlc3
|
UTSW |
2 |
139,336,154 (GRCm39) |
missense |
probably benign |
0.17 |
R9237:Sptlc3
|
UTSW |
2 |
139,408,605 (GRCm39) |
missense |
probably benign |
0.40 |
R9319:Sptlc3
|
UTSW |
2 |
139,478,730 (GRCm39) |
missense |
possibly damaging |
0.65 |
R9330:Sptlc3
|
UTSW |
2 |
139,388,423 (GRCm39) |
missense |
probably benign |
|
|
Predicted Primers |
PCR Primer
(F):5'- GCAAGCAATTGCCCTTTTCTTG -3'
(R):5'- GGATATTGCTGACATACCACAGTG -3'
Sequencing Primer
(F):5'- GTGTGGGAGAAAGATTAATCTTCC -3'
(R):5'- CACAGTGGTTTGTTGTTGTTTATTTG -3'
|
Posted On |
2016-06-21 |