Incidental Mutation 'R2396:Sptlc3'
| ID |
248512 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sptlc3
|
| Ensembl Gene |
ENSMUSG00000039092 |
| Gene Name |
serine palmitoyltransferase, long chain base subunit 3 |
| Synonyms |
C130053K05Rik |
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.122)
|
| Stock # |
R2396 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 139408506 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 207
(I207T)
|
| 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: I207T
PolyPhen 2
Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: I207T
| 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: I207T
PolyPhen 2
Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: I207T
| 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
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.8%
- 20x: 93.3%
|
| 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: 24 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamtsl1 |
G |
A |
4: 86,261,356 (GRCm39) |
W1189* |
probably null |
Het |
| Col4a4 |
C |
G |
1: 82,484,793 (GRCm39) |
M491I |
unknown |
Het |
| Col5a1 |
C |
A |
2: 27,876,741 (GRCm39) |
D813E |
unknown |
Het |
| Cyp4b1 |
T |
C |
4: 115,498,843 (GRCm39) |
Y113C |
probably benign |
Het |
| Dmac1 |
A |
G |
4: 75,196,458 (GRCm39) |
F11L |
unknown |
Het |
| Dnah9 |
G |
T |
11: 65,975,984 (GRCm39) |
T1355K |
probably benign |
Het |
| Efemp1 |
G |
A |
11: 28,817,941 (GRCm39) |
R140Q |
possibly damaging |
Het |
| Elapor2 |
T |
C |
5: 9,485,395 (GRCm39) |
L519P |
possibly damaging |
Het |
| Fndc3a |
T |
C |
14: 72,921,123 (GRCm39) |
D17G |
possibly damaging |
Het |
| Grm8 |
C |
T |
6: 27,761,241 (GRCm39) |
A328T |
probably damaging |
Het |
| Lepr |
C |
A |
4: 101,590,725 (GRCm39) |
A101E |
probably benign |
Het |
| Ncapg |
A |
G |
5: 45,835,715 (GRCm39) |
N382S |
probably benign |
Het |
| Or10am5 |
C |
A |
7: 6,517,784 (GRCm39) |
V215F |
probably damaging |
Het |
| Or5m13b |
T |
C |
2: 85,754,269 (GRCm39) |
I219T |
probably benign |
Het |
| Pacs2 |
G |
A |
12: 113,026,987 (GRCm39) |
D605N |
probably damaging |
Het |
| Pigb |
T |
A |
9: 72,922,553 (GRCm39) |
R11* |
probably null |
Het |
| Prl8a1 |
C |
A |
13: 27,758,007 (GRCm39) |
R234L |
probably benign |
Het |
| Spred3 |
T |
C |
7: 28,866,059 (GRCm39) |
H80R |
probably damaging |
Het |
| Tll1 |
C |
A |
8: 64,523,324 (GRCm39) |
G463* |
probably null |
Het |
| Tm4sf4 |
T |
G |
3: 57,345,181 (GRCm39) |
C196G |
unknown |
Het |
| Tmem87a |
A |
T |
2: 120,234,540 (GRCm39) |
M1K |
probably null |
Het |
| Tmem92 |
A |
G |
11: 94,673,233 (GRCm39) |
L10P |
probably damaging |
Het |
| Trdn |
A |
T |
10: 33,071,978 (GRCm39) |
E215V |
probably damaging |
Het |
| Trpm2 |
A |
T |
10: 77,766,471 (GRCm39) |
D849E |
probably benign |
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 |
|
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 |
|
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'- ATAGGCTACATTCAACTGTGTTTCC -3'
(R):5'- TGCCAACGCTTTTGATAAAGG -3'
Sequencing Primer
(F):5'- ggtctgtgttggtgtatg -3'
(R):5'- CTTGGGAGTGGTATAGCAG -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation