Incidental Mutation 'R2972:Sptlc3'
ID |
255236 |
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 # |
R2972 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
2 |
Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 139431581 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 368
(T368A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000105710
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047370]
[ENSMUST00000110083]
|
AlphaFold |
Q8BG54 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000047370
AA Change: T368A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000048313 Gene: ENSMUSG00000039092 AA Change: T368A
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 damaging
Transcript: ENSMUST00000110083
AA Change: T368A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000105710 Gene: ENSMUSG00000039092 AA Change: T368A
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
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184747
|
Meta Mutation Damage Score |
0.9207 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
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: 25 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
BC048507 |
T |
C |
13: 68,011,749 (GRCm39) |
I42T |
probably benign |
Het |
Card9 |
C |
T |
2: 26,247,222 (GRCm39) |
R309H |
probably damaging |
Het |
Clec14a |
T |
A |
12: 58,314,360 (GRCm39) |
R421W |
probably damaging |
Het |
Crnkl1 |
A |
G |
2: 145,774,181 (GRCm39) |
L94P |
probably benign |
Het |
D930007J09Rik |
C |
T |
13: 32,986,742 (GRCm39) |
|
probably benign |
Het |
Dhrs7c |
T |
A |
11: 67,706,697 (GRCm39) |
I285N |
possibly damaging |
Het |
Golga2 |
A |
G |
2: 32,195,671 (GRCm39) |
N752S |
probably benign |
Het |
Klrb1-ps1 |
A |
G |
6: 129,096,719 (GRCm39) |
|
noncoding transcript |
Het |
Nin |
G |
A |
12: 70,109,487 (GRCm39) |
R151C |
probably damaging |
Het |
Nsun6 |
A |
C |
2: 15,042,883 (GRCm39) |
|
probably null |
Het |
Nyap2 |
C |
T |
1: 81,169,485 (GRCm39) |
R81* |
probably null |
Het |
Or1n2 |
G |
A |
2: 36,797,416 (GRCm39) |
V153M |
probably benign |
Het |
Or4a69 |
G |
T |
2: 89,313,120 (GRCm39) |
R120S |
possibly damaging |
Het |
Pkhd1l1 |
T |
A |
15: 44,410,644 (GRCm39) |
M2717K |
possibly damaging |
Het |
Ralgapa1 |
T |
C |
12: 55,867,540 (GRCm39) |
K5E |
possibly damaging |
Het |
Rnf130 |
T |
A |
11: 49,984,627 (GRCm39) |
L309* |
probably null |
Het |
Rsf1 |
ATGGCG |
ATGGCGACGGTGGCG |
7: 97,229,111 (GRCm39) |
|
probably benign |
Het |
Rxrg |
G |
A |
1: 167,466,715 (GRCm39) |
R422H |
probably damaging |
Het |
Serpinb9e |
T |
A |
13: 33,439,126 (GRCm39) |
V184E |
probably benign |
Het |
Slc10a5 |
A |
T |
3: 10,399,517 (GRCm39) |
I381N |
probably damaging |
Het |
Slit1 |
G |
A |
19: 41,599,455 (GRCm39) |
P1032L |
probably benign |
Het |
Ubr4 |
T |
C |
4: 139,133,847 (GRCm39) |
Y748H |
probably benign |
Het |
Ugt8a |
T |
C |
3: 125,708,957 (GRCm39) |
H51R |
probably benign |
Het |
Vmn2r117 |
A |
G |
17: 23,678,830 (GRCm39) |
V798A |
probably damaging |
Het |
Vmn2r77 |
T |
C |
7: 86,452,893 (GRCm39) |
Y537H |
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 |
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'- TGTGCTAGCATGGAAGGTTC -3'
(R):5'- CTCCCAGGTACTCTACACAGTTTG -3'
Sequencing Primer
(F):5'- CCATTGTGAACCTTGCCCAGATAG -3'
(R):5'- CCAGGTACTCTACACAGTTTGTTATG -3'
|
Posted On |
2014-12-29 |