Incidental Mutation 'R9237:Sptlc3'
| ID |
700526 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sptlc3
|
| Ensembl Gene |
ENSMUSG00000039092 |
| Gene Name |
serine palmitoyltransferase, long chain base subunit 3 |
| Synonyms |
C130053K05Rik |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.122)
|
| Stock # |
R9237 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 139408605 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Glutamic Acid
at position 240
(V240E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000048313
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047370]
[ENSMUST00000110083]
|
| AlphaFold |
Q8BG54 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000047370
AA Change: V240E
PolyPhen 2
Score 0.397 (Sensitivity: 0.89; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: V240E
| 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: V240E
PolyPhen 2
Score 0.397 (Sensitivity: 0.89; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: V240E
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
60 |
79 |
N/A |
INTRINSIC |
|
Pfam:Aminotran_1_2
|
160 |
520 |
4.8e-59 |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
| Validation Efficiency |
|
| 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca12 |
A |
T |
1: 71,318,557 (GRCm39) |
N1815K |
probably damaging |
Het |
| Acat1 |
C |
A |
9: 53,494,816 (GRCm39) |
A359S |
probably damaging |
Het |
| Actn1 |
T |
C |
12: 80,240,470 (GRCm39) |
N206D |
possibly damaging |
Het |
| Adgrf4 |
T |
A |
17: 42,980,782 (GRCm39) |
H101L |
probably benign |
Het |
| Ager |
T |
A |
17: 34,816,869 (GRCm39) |
M1K |
probably null |
Het |
| Akap12 |
T |
C |
10: 4,307,231 (GRCm39) |
I1452T |
probably benign |
Het |
| Arap3 |
G |
A |
18: 38,112,934 (GRCm39) |
A1092V |
possibly damaging |
Het |
| Bnip5 |
T |
C |
17: 29,123,522 (GRCm39) |
E392G |
probably benign |
Het |
| C8b |
A |
G |
4: 104,650,481 (GRCm39) |
T430A |
probably benign |
Het |
| Dars2 |
G |
A |
1: 160,873,025 (GRCm39) |
R455W |
probably damaging |
Het |
| Erbb4 |
T |
G |
1: 68,081,601 (GRCm39) |
Q1144H |
possibly damaging |
Het |
| Exoc2 |
G |
A |
13: 31,048,858 (GRCm39) |
H732Y |
probably benign |
Het |
| Fhad1 |
T |
A |
4: 141,632,483 (GRCm39) |
M1219L |
probably benign |
Het |
| Fktn |
G |
A |
4: 53,734,854 (GRCm39) |
G125D |
probably benign |
Het |
| Gna15 |
T |
C |
10: 81,359,683 (GRCm39) |
K36E |
possibly damaging |
Het |
| Gpr156 |
C |
T |
16: 37,825,648 (GRCm39) |
Q622* |
probably null |
Het |
| Grip1 |
C |
T |
10: 119,911,310 (GRCm39) |
S1091L |
probably benign |
Het |
| H4c12 |
A |
G |
13: 21,934,534 (GRCm39) |
S48P |
probably damaging |
Het |
| Helt |
A |
G |
8: 46,745,536 (GRCm39) |
F154L |
probably benign |
Het |
| Ide |
T |
C |
19: 37,307,898 (GRCm39) |
N38S |
|
Het |
| Ighg2b |
A |
T |
12: 113,270,217 (GRCm39) |
V267E |
|
Het |
| Map3k10 |
C |
T |
7: 27,357,842 (GRCm39) |
W645* |
probably null |
Het |
| Mcrip1 |
G |
A |
11: 120,435,542 (GRCm39) |
P31L |
probably damaging |
Het |
| Mttp |
T |
C |
3: 137,810,444 (GRCm39) |
E657G |
probably benign |
Het |
| Myom1 |
C |
T |
17: 71,408,051 (GRCm39) |
T1195I |
probably damaging |
Het |
| Myom2 |
T |
C |
8: 15,152,591 (GRCm39) |
V646A |
possibly damaging |
Het |
| Nlrc3 |
A |
T |
16: 3,783,073 (GRCm39) |
M128K |
probably benign |
Het |
| Nr2f6 |
A |
C |
8: 71,831,073 (GRCm39) |
C112W |
probably damaging |
Het |
| Or5af1 |
A |
T |
11: 58,722,057 (GRCm39) |
I26F |
possibly damaging |
Het |
| Or5m13b |
T |
A |
2: 85,754,267 (GRCm39) |
Y218* |
probably null |
Het |
| P2rx3 |
T |
C |
2: 84,853,896 (GRCm39) |
N139S |
probably benign |
Het |
| Pcdha11 |
T |
A |
18: 37,145,260 (GRCm39) |
N450K |
probably damaging |
Het |
| Phb1 |
T |
C |
11: 95,566,034 (GRCm39) |
I106T |
possibly damaging |
Het |
| Phyhipl |
C |
A |
10: 70,406,720 (GRCm39) |
R78L |
possibly damaging |
Het |
| Pmfbp1 |
A |
G |
8: 110,246,932 (GRCm39) |
D268G |
probably damaging |
Het |
| Pramel39-ps |
G |
T |
5: 94,451,001 (GRCm39) |
P375H |
probably damaging |
Het |
| Rcbtb2 |
C |
A |
14: 73,411,936 (GRCm39) |
H408Q |
probably damaging |
Het |
| Sptbn1 |
A |
T |
11: 30,096,803 (GRCm39) |
V271E |
probably damaging |
Het |
| Stat4 |
A |
G |
1: 52,146,073 (GRCm39) |
N742S |
probably benign |
Het |
| Tas2r118 |
T |
A |
6: 23,969,617 (GRCm39) |
Y148F |
probably benign |
Het |
| Trmt5 |
G |
T |
12: 73,331,568 (GRCm39) |
Q163K |
probably benign |
Het |
| Ube2d1 |
T |
A |
10: 71,097,925 (GRCm39) |
I37F |
probably damaging |
Het |
| Vmn1r43 |
G |
A |
6: 89,846,877 (GRCm39) |
T203M |
probably damaging |
Het |
| Vps13b |
C |
T |
15: 35,841,479 (GRCm39) |
P2503L |
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 |
|
R5162:Sptlc3
|
UTSW |
2 |
139,473,263 (GRCm39) |
missense |
probably benign |
0.11 |
|
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 |
|
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'- CTTGCTATGCTACAGGTCTGTG -3'
(R):5'- TACCTGGGAGTATCACAATCAAAAG -3'
Sequencing Primer
(F):5'- CTATGCTACAGGTCTGTGTTGGTG -3'
(R):5'- AGGATCCTTTTGCCAACG -3'
|
| Posted On |
2022-02-07 |
Incidental Mutation