Incidental Mutation 'R9330:Sptlc3'
| ID |
706774 |
| 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 # |
R9330 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 139388423 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Isoleucine
at position 138
(M138I)
|
| 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: M138I
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: M138I
| 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: M138I
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: M138I
| 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: 99.0%
|
| Validation Efficiency |
100% (52/52) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2900026A02Rik |
T |
A |
5: 113,330,833 (GRCm39) |
D1127V |
probably benign |
Het |
| Ajap1 |
A |
G |
4: 153,516,961 (GRCm39) |
S127P |
probably damaging |
Het |
| Cdon |
T |
A |
9: 35,400,275 (GRCm39) |
Y996* |
probably null |
Het |
| Cnr2 |
A |
G |
4: 135,644,312 (GRCm39) |
D130G |
probably damaging |
Het |
| Cyp2j12 |
A |
G |
4: 95,994,791 (GRCm39) |
V344A |
probably damaging |
Het |
| Cyp4a32 |
T |
A |
4: 115,478,635 (GRCm39) |
C456S |
probably damaging |
Het |
| Dipk1a |
A |
T |
5: 108,059,583 (GRCm39) |
D123E |
probably benign |
Het |
| Dsc1 |
T |
A |
18: 20,243,214 (GRCm39) |
T80S |
possibly damaging |
Het |
| Esyt2 |
G |
A |
12: 116,305,765 (GRCm39) |
V332I |
probably benign |
Het |
| Fcgbpl1 |
C |
T |
7: 27,856,410 (GRCm39) |
H2066Y |
probably benign |
Het |
| G2e3 |
C |
T |
12: 51,403,928 (GRCm39) |
Q161* |
probably null |
Het |
| Galnt18 |
C |
A |
7: 111,071,271 (GRCm39) |
R566L |
probably benign |
Het |
| Gatb |
C |
T |
3: 85,559,801 (GRCm39) |
P542S |
probably benign |
Het |
| Gpt |
G |
A |
15: 76,581,215 (GRCm39) |
R53H |
possibly damaging |
Het |
| Herpud2 |
T |
C |
9: 25,036,246 (GRCm39) |
E138G |
probably damaging |
Het |
| Hivep1 |
A |
G |
13: 42,317,713 (GRCm39) |
Y2063C |
probably damaging |
Het |
| Hoxd12 |
T |
A |
2: 74,505,733 (GRCm39) |
Y101* |
probably null |
Het |
| Hps4 |
G |
A |
5: 112,525,905 (GRCm39) |
S642N |
possibly damaging |
Het |
| Lama4 |
T |
C |
10: 38,954,722 (GRCm39) |
F1092L |
probably damaging |
Het |
| Lrp1b |
A |
G |
2: 41,012,993 (GRCm39) |
S1985P |
|
Het |
| Malrd1 |
C |
T |
2: 16,260,089 (GRCm39) |
P2103L |
unknown |
Het |
| Mbnl1 |
C |
A |
3: 60,511,168 (GRCm39) |
N41K |
possibly damaging |
Het |
| Muc16 |
T |
C |
9: 18,552,332 (GRCm39) |
N4654D |
probably benign |
Het |
| Mug1 |
A |
G |
6: 121,859,723 (GRCm39) |
T1241A |
probably benign |
Het |
| Ncam1 |
T |
C |
9: 49,456,097 (GRCm39) |
D507G |
probably benign |
Het |
| Nfxl1 |
A |
T |
5: 72,681,451 (GRCm39) |
D693E |
probably benign |
Het |
| Npr1 |
A |
T |
3: 90,365,979 (GRCm39) |
I604N |
possibly damaging |
Het |
| Obscn |
G |
A |
11: 58,971,047 (GRCm39) |
H2280Y |
possibly damaging |
Het |
| Or5b105 |
T |
A |
19: 13,080,588 (GRCm39) |
I27F |
probably benign |
Het |
| Or7c70 |
T |
C |
10: 78,683,153 (GRCm39) |
T199A |
probably benign |
Het |
| Pcdh10 |
T |
C |
3: 45,335,618 (GRCm39) |
V644A |
probably damaging |
Het |
| Pgk2 |
T |
A |
17: 40,519,078 (GRCm39) |
I117F |
probably benign |
Het |
| Pinx1 |
T |
A |
14: 64,109,777 (GRCm39) |
S110T |
probably benign |
Het |
| Pira1 |
A |
T |
7: 3,742,234 (GRCm39) |
C98S |
probably damaging |
Het |
| Psmd1 |
A |
G |
1: 86,061,490 (GRCm39) |
Y900C |
probably damaging |
Het |
| Rab3a |
C |
T |
8: 71,209,881 (GRCm39) |
R149C |
probably damaging |
Het |
| Samsn1 |
T |
A |
16: 75,673,433 (GRCm39) |
N148Y |
probably damaging |
Het |
| Sin3a |
C |
T |
9: 57,032,481 (GRCm39) |
R1142C |
probably damaging |
Het |
| Snrnp27 |
A |
G |
6: 86,653,184 (GRCm39) |
C145R |
probably benign |
Het |
| Sorl1 |
A |
C |
9: 41,979,229 (GRCm39) |
V423G |
probably damaging |
Het |
| Tex15 |
T |
A |
8: 34,065,143 (GRCm39) |
F1524L |
probably benign |
Het |
| Tln2 |
T |
C |
9: 67,229,213 (GRCm39) |
N113D |
possibly damaging |
Het |
| Tmco1 |
C |
T |
1: 167,136,132 (GRCm39) |
|
probably benign |
Het |
| Tnfsf14 |
T |
A |
17: 57,501,020 (GRCm39) |
D17V |
probably damaging |
Het |
| Trmt44 |
T |
C |
5: 35,727,264 (GRCm39) |
D317G |
probably damaging |
Het |
| Trpc2 |
T |
C |
7: 101,739,764 (GRCm39) |
F563L |
probably benign |
Het |
| Ubox5 |
T |
C |
2: 130,442,165 (GRCm39) |
K174R |
probably benign |
Het |
| Vrk3 |
T |
C |
7: 44,424,910 (GRCm39) |
S442P |
probably damaging |
Het |
| Wdr64 |
A |
T |
1: 175,554,024 (GRCm39) |
T185S |
possibly damaging |
Het |
| Wfdc15a |
A |
T |
2: 164,041,632 (GRCm39) |
C64S |
probably damaging |
Het |
| Zfp688 |
A |
G |
7: 127,021,077 (GRCm39) |
Y34H |
probably damaging |
Het |
| Zfp808 |
A |
T |
13: 62,319,974 (GRCm39) |
H401L |
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 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGATTAACCAGGCCCTTCC -3'
(R):5'- CCACCATAGCATGAGAAATTGC -3'
Sequencing Primer
(F):5'- GCAAATAAGGTCTTTTTCCAGAGG -3'
(R):5'- CACCATAGCATGAGAAATTGCAAAGG -3'
|
| Posted On |
2022-04-18 |
Incidental Mutation