Incidental Mutation 'R5840:Sptlc3'
ID |
450360 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sptlc3
|
Ensembl Gene |
ENSMUSG00000039092 |
Gene Name |
serine palmitoyltransferase, long chain base subunit 3 |
Synonyms |
C130053K05Rik |
MMRRC Submission |
044060-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.122)
|
Stock # |
R5840 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 139389126 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Tyrosine
at position 169
(N169Y)
|
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: N169Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000048313 Gene: ENSMUSG00000039092 AA Change: N169Y
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: N169Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000105710 Gene: ENSMUSG00000039092 AA Change: N169Y
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
|
Meta Mutation Damage Score |
0.9551 |
Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.3%
- 10x: 96.5%
- 20x: 88.1%
|
Validation Efficiency |
99% (75/76) |
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: 60 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca2 |
G |
A |
2: 25,323,371 (GRCm39) |
R113Q |
probably benign |
Het |
Aip |
G |
A |
19: 4,166,010 (GRCm39) |
P147L |
possibly damaging |
Het |
Anapc1 |
A |
C |
2: 128,448,957 (GRCm39) |
|
probably benign |
Het |
Arhgap42 |
C |
T |
9: 9,046,518 (GRCm39) |
V240I |
possibly damaging |
Het |
Axdnd1 |
T |
C |
1: 156,176,528 (GRCm39) |
E684G |
probably damaging |
Het |
BC005624 |
G |
A |
2: 30,871,869 (GRCm39) |
R2W |
probably benign |
Het |
Cd177 |
T |
G |
7: 24,457,495 (GRCm39) |
Q182P |
probably damaging |
Het |
Cdca5 |
G |
A |
19: 6,140,399 (GRCm39) |
E187K |
possibly damaging |
Het |
Chmp1a |
T |
C |
8: 123,934,839 (GRCm39) |
Q39R |
probably benign |
Het |
Dab2ip |
A |
G |
2: 35,617,511 (GRCm39) |
I1079V |
probably damaging |
Het |
Dip2c |
A |
T |
13: 9,556,712 (GRCm39) |
E85D |
possibly damaging |
Het |
Elmo2 |
A |
T |
2: 165,137,472 (GRCm39) |
S497R |
possibly damaging |
Het |
Ephb6 |
C |
T |
6: 41,592,507 (GRCm39) |
A339V |
possibly damaging |
Het |
Foxred1 |
T |
C |
9: 35,121,435 (GRCm39) |
K38E |
probably damaging |
Het |
Frem2 |
T |
A |
3: 53,555,342 (GRCm39) |
T1732S |
probably damaging |
Het |
Fto |
A |
G |
8: 92,393,068 (GRCm39) |
|
probably benign |
Het |
Gm17430 |
T |
A |
18: 9,726,528 (GRCm39) |
Q48L |
probably damaging |
Het |
Gng2 |
A |
G |
14: 19,925,882 (GRCm39) |
I70T |
probably damaging |
Het |
Gtf2a2 |
A |
G |
9: 69,922,575 (GRCm39) |
|
probably benign |
Het |
Invs |
A |
G |
4: 48,396,284 (GRCm39) |
D263G |
probably damaging |
Het |
Itga2b |
C |
T |
11: 102,352,157 (GRCm39) |
V475M |
probably damaging |
Het |
Kansl1l |
A |
G |
1: 66,809,374 (GRCm39) |
|
probably benign |
Het |
Klhl25 |
T |
C |
7: 75,516,440 (GRCm39) |
F449L |
possibly damaging |
Het |
Lamb1 |
T |
A |
12: 31,316,755 (GRCm39) |
C83S |
probably damaging |
Het |
Loxl4 |
G |
T |
19: 42,587,154 (GRCm39) |
T648K |
probably damaging |
Het |
Lrit2 |
T |
C |
14: 36,790,962 (GRCm39) |
F214L |
possibly damaging |
Het |
N4bp2 |
T |
G |
5: 65,965,437 (GRCm39) |
L1162R |
probably damaging |
Het |
Naa40 |
A |
T |
19: 7,207,373 (GRCm39) |
I117N |
probably benign |
Het |
Ncapd3 |
T |
C |
9: 27,006,054 (GRCm39) |
S1492P |
probably benign |
Het |
Nf2 |
T |
A |
11: 4,766,146 (GRCm39) |
D128V |
probably benign |
Het |
Nox4 |
T |
C |
7: 87,010,001 (GRCm39) |
S401P |
probably benign |
Het |
Nt5c1b |
T |
C |
12: 10,427,171 (GRCm39) |
V323A |
probably damaging |
Het |
Or52a33 |
C |
T |
7: 103,288,463 (GRCm39) |
V295I |
probably benign |
Het |
Or52s19 |
T |
A |
7: 103,007,576 (GRCm39) |
H275L |
probably damaging |
Het |
Or5b118 |
G |
A |
19: 13,449,242 (GRCm39) |
V303I |
probably benign |
Het |
Pcdhb14 |
T |
C |
18: 37,581,803 (GRCm39) |
V303A |
probably benign |
Het |
Pde8a |
C |
A |
7: 80,863,713 (GRCm39) |
H17Q |
probably benign |
Het |
Pfkl |
C |
T |
10: 77,824,558 (GRCm39) |
V716I |
probably benign |
Het |
Phc3 |
G |
A |
3: 30,990,732 (GRCm39) |
S495L |
possibly damaging |
Het |
Psg18 |
A |
G |
7: 18,080,527 (GRCm39) |
|
probably benign |
Het |
Rcc2 |
T |
G |
4: 140,439,449 (GRCm39) |
N175K |
possibly damaging |
Het |
Rhot2 |
G |
A |
17: 26,059,032 (GRCm39) |
T276I |
probably benign |
Het |
Rnase9 |
A |
T |
14: 51,276,445 (GRCm39) |
Y178N |
probably benign |
Het |
Sema4b |
T |
C |
7: 79,868,697 (GRCm39) |
C297R |
probably damaging |
Het |
Slc35d2 |
T |
C |
13: 64,266,227 (GRCm39) |
|
probably null |
Het |
Srsf9 |
T |
G |
5: 115,469,524 (GRCm39) |
M29R |
probably benign |
Het |
Stip1 |
C |
A |
19: 6,999,436 (GRCm39) |
D449Y |
possibly damaging |
Het |
Syne2 |
T |
A |
12: 75,927,065 (GRCm39) |
|
probably null |
Het |
Tgm5 |
A |
G |
2: 120,916,141 (GRCm39) |
|
probably null |
Het |
Thbs2 |
A |
T |
17: 14,901,692 (GRCm39) |
|
probably null |
Het |
Trak2 |
T |
C |
1: 58,958,432 (GRCm39) |
E283G |
probably damaging |
Het |
Trbv21 |
A |
G |
6: 41,179,792 (GRCm39) |
Y36C |
probably damaging |
Het |
Trpm7 |
A |
T |
2: 126,664,531 (GRCm39) |
Y949* |
probably null |
Het |
Ubqln5 |
T |
C |
7: 103,778,161 (GRCm39) |
D221G |
possibly damaging |
Het |
Ubxn4 |
T |
A |
1: 128,187,262 (GRCm39) |
V85D |
possibly damaging |
Het |
Vmn1r172 |
T |
A |
7: 23,359,600 (GRCm39) |
W162R |
probably benign |
Het |
Vrk2 |
A |
G |
11: 26,484,314 (GRCm39) |
|
probably benign |
Het |
Zc3h8 |
A |
C |
2: 128,771,824 (GRCm39) |
D276E |
probably benign |
Het |
Zfp369 |
C |
T |
13: 65,445,092 (GRCm39) |
T745I |
possibly damaging |
Het |
Zfp608 |
T |
C |
18: 55,031,978 (GRCm39) |
K654R |
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 |
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'- GCCTGGAACTCTCACTAATGC -3'
(R):5'- CAGCCTTGACACTGTCAGAATTTG -3'
Sequencing Primer
(F):5'- TGGAACTCTCACTAATGCTATGTC -3'
(R):5'- CATTTCATTTCTGGTGCTGG -3'
|
Posted On |
2016-12-20 |