Incidental Mutation 'R2093:Sptlc3'
| ID |
231896 |
| 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 # |
R2093 (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 T
at 139467794 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Phenylalanine
at position 451
(I451F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105710
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047370]
[ENSMUST00000110083]
|
| AlphaFold |
Q8BG54 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000047370
AA Change: I451F
PolyPhen 2
Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: I451F
| 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 |
possibly damaging
Transcript: ENSMUST00000110083
AA Change: I451F
PolyPhen 2
Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: I451F
| 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: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.7%
|
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| AA986860 |
A |
G |
1: 130,671,041 (GRCm39) |
D421G |
probably benign |
Het |
| Adamts1 |
T |
G |
16: 85,599,333 (GRCm39) |
Q89P |
probably benign |
Het |
| Arhgef10l |
T |
G |
4: 140,297,601 (GRCm39) |
N277T |
possibly damaging |
Het |
| Atp2c1 |
G |
A |
9: 105,295,320 (GRCm39) |
R669* |
probably null |
Het |
| Brip1 |
T |
C |
11: 86,029,971 (GRCm39) |
T558A |
possibly damaging |
Het |
| Cbr2 |
G |
A |
11: 120,621,255 (GRCm39) |
T148I |
probably benign |
Het |
| Ccdc110 |
C |
A |
8: 46,395,114 (GRCm39) |
T335K |
probably damaging |
Het |
| Cd44 |
T |
G |
2: 102,644,629 (GRCm39) |
D731A |
probably damaging |
Het |
| Cnot1 |
T |
C |
8: 96,501,986 (GRCm39) |
D44G |
probably damaging |
Het |
| Cnrip1 |
T |
C |
11: 17,002,237 (GRCm39) |
V23A |
probably damaging |
Het |
| Cntnap5c |
A |
T |
17: 58,505,995 (GRCm39) |
H673L |
probably benign |
Het |
| Col3a1 |
C |
T |
1: 45,372,150 (GRCm39) |
A493V |
probably damaging |
Het |
| Crem |
A |
T |
18: 3,299,256 (GRCm39) |
V19E |
probably damaging |
Het |
| Cyp2g1 |
A |
G |
7: 26,518,858 (GRCm39) |
D418G |
probably benign |
Het |
| Dmrta1 |
A |
T |
4: 89,579,742 (GRCm39) |
H234L |
probably benign |
Het |
| Drc3 |
C |
T |
11: 60,261,310 (GRCm39) |
R154W |
probably damaging |
Het |
| Drgx |
C |
T |
14: 32,369,112 (GRCm39) |
|
probably benign |
Het |
| Eef1d |
A |
G |
15: 75,774,550 (GRCm39) |
S370P |
probably benign |
Het |
| Fdx2 |
T |
C |
9: 20,984,720 (GRCm39) |
H28R |
probably benign |
Het |
| Fmo5 |
A |
G |
3: 97,553,194 (GRCm39) |
I381V |
probably benign |
Het |
| Fpr-rs4 |
CAGGAA |
CA |
17: 18,242,596 (GRCm39) |
|
probably null |
Het |
| Fras1 |
T |
C |
5: 96,929,062 (GRCm39) |
L3822P |
probably damaging |
Het |
| Gm3604 |
G |
T |
13: 62,517,420 (GRCm39) |
H313N |
possibly damaging |
Het |
| Heatr4 |
T |
C |
12: 84,021,855 (GRCm39) |
E460G |
possibly damaging |
Het |
| Ino80 |
T |
A |
2: 119,257,151 (GRCm39) |
H834L |
possibly damaging |
Het |
| Insr |
A |
T |
8: 3,254,762 (GRCm39) |
C331S |
probably damaging |
Het |
| Itih4 |
C |
T |
14: 30,613,694 (GRCm39) |
L304F |
probably damaging |
Het |
| Klhdc3 |
C |
T |
17: 46,988,879 (GRCm39) |
V104I |
probably benign |
Het |
| Lrp2 |
C |
T |
2: 69,366,365 (GRCm39) |
D245N |
probably benign |
Het |
| Map1b |
T |
C |
13: 99,566,178 (GRCm39) |
E2181G |
unknown |
Het |
| Map2 |
T |
C |
1: 66,438,599 (GRCm39) |
V41A |
probably damaging |
Het |
| Mical3 |
A |
T |
6: 121,017,347 (GRCm39) |
H156Q |
probably damaging |
Het |
| Mrgpra2b |
C |
T |
7: 47,113,908 (GRCm39) |
V249I |
probably benign |
Het |
| Myo5b |
T |
A |
18: 74,892,263 (GRCm39) |
L1669Q |
probably damaging |
Het |
| Nme8 |
G |
A |
13: 19,835,042 (GRCm39) |
S548F |
probably damaging |
Het |
| Npas1 |
A |
T |
7: 16,193,202 (GRCm39) |
N408K |
probably benign |
Het |
| Or1j11 |
A |
T |
2: 36,311,941 (GRCm39) |
Y177F |
probably benign |
Het |
| Or8k30 |
A |
C |
2: 86,339,587 (GRCm39) |
Q261H |
probably damaging |
Het |
| Pcnx4 |
T |
C |
12: 72,626,216 (GRCm39) |
Y1141H |
probably damaging |
Het |
| Pmaip1 |
C |
A |
18: 66,594,052 (GRCm39) |
P64Q |
probably damaging |
Het |
| Ranbp3 |
T |
A |
17: 57,017,145 (GRCm39) |
M387K |
probably damaging |
Het |
| Rbm4 |
A |
G |
19: 4,837,792 (GRCm39) |
Y231H |
probably damaging |
Het |
| Rpgrip1l |
T |
C |
8: 91,996,760 (GRCm39) |
S105G |
possibly damaging |
Het |
| Rsf1 |
CG |
CGACGGCGGGG |
7: 97,229,115 (GRCm39) |
|
probably benign |
Het |
| Rtn3 |
A |
T |
19: 7,434,215 (GRCm39) |
D573E |
probably damaging |
Het |
| Rxrg |
T |
C |
1: 167,454,893 (GRCm39) |
C159R |
probably damaging |
Het |
| Sdk2 |
T |
C |
11: 113,833,948 (GRCm39) |
Y78C |
probably damaging |
Het |
| Smu1 |
A |
G |
4: 40,738,438 (GRCm39) |
V432A |
probably benign |
Het |
| Spag1 |
T |
C |
15: 36,224,276 (GRCm39) |
L609P |
probably damaging |
Het |
| Spata21 |
T |
G |
4: 140,824,277 (GRCm39) |
V180G |
probably benign |
Het |
| Spata31e2 |
G |
T |
1: 26,721,222 (GRCm39) |
Y1319* |
probably null |
Het |
| Srl |
A |
G |
16: 4,340,896 (GRCm39) |
C8R |
unknown |
Het |
| Tmprss13 |
A |
G |
9: 45,256,340 (GRCm39) |
R485G |
probably damaging |
Het |
| Trpv4 |
C |
T |
5: 114,773,565 (GRCm39) |
A266T |
probably damaging |
Het |
| Vmn1r198 |
A |
G |
13: 22,538,855 (GRCm39) |
T25A |
probably benign |
Het |
| Vmn2r77 |
T |
C |
7: 86,450,702 (GRCm39) |
V196A |
probably benign |
Het |
| Vmn2r82 |
C |
T |
10: 79,231,813 (GRCm39) |
T604I |
probably benign |
Het |
| Zfp268 |
C |
A |
4: 145,349,139 (GRCm39) |
T192N |
probably benign |
Het |
| Zfp354a |
C |
T |
11: 50,960,551 (GRCm39) |
T254I |
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 |
|
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 |
|
R9330:Sptlc3
|
UTSW |
2 |
139,388,423 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGTCTCCTAGGCACAACACAG -3'
(R):5'- GAGGTCAGAACTCAAGTACCTCAC -3'
Sequencing Primer
(F):5'- ACAGTACTTGTGTCTGATCACC -3'
(R):5'- CCAAGCACACAATCTAGTTCATG -3'
|
| Posted On |
2014-09-18 |
Incidental Mutation