Incidental Mutation 'R7826:Sptlc3'
ID |
602171 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Sptlc3
|
Ensembl Gene |
ENSMUSG00000039092 |
Gene Name |
serine palmitoyltransferase, long chain base subunit 3 |
Synonyms |
C130053K05Rik |
MMRRC Submission |
045880-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.122)
|
Stock # |
R7826 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
139335833-139478981 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 139389115 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Threonine
at position 165
(M165T)
|
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: M165T
PolyPhen 2
Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000048313 Gene: ENSMUSG00000039092 AA Change: M165T
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: M165T
PolyPhen 2
Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000105710 Gene: ENSMUSG00000039092 AA Change: M165T
Domain | Start | End | E-Value | Type |
transmembrane domain
|
60 |
79 |
N/A |
INTRINSIC |
Pfam:Aminotran_1_2
|
160 |
520 |
4.8e-59 |
PFAM |
|
Meta Mutation Damage Score |
0.3596 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
Validation Efficiency |
100% (60/60) |
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: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Ajm1 |
C |
A |
2: 25,468,477 (GRCm39) |
R478L |
possibly damaging |
Het |
Arhgap27 |
T |
C |
11: 103,229,153 (GRCm39) |
T521A |
probably benign |
Het |
Bean1 |
CT |
C |
8: 104,908,664 (GRCm39) |
|
probably null |
Het |
Btbd9 |
A |
T |
17: 30,553,301 (GRCm39) |
I387N |
probably benign |
Het |
Ccdc27 |
C |
T |
4: 154,123,958 (GRCm39) |
|
probably null |
Het |
Ccdc88a |
A |
T |
11: 29,453,563 (GRCm39) |
H1642L |
probably benign |
Het |
Cd300c2 |
C |
T |
11: 114,891,644 (GRCm39) |
V77I |
possibly damaging |
Het |
Chrnb2 |
A |
T |
3: 89,670,550 (GRCm39) |
S63T |
probably damaging |
Het |
Dlgap2 |
C |
T |
8: 14,793,410 (GRCm39) |
P467L |
probably benign |
Het |
Dnah5 |
C |
T |
15: 28,367,958 (GRCm39) |
T2781M |
probably damaging |
Het |
Donson |
T |
C |
16: 91,485,344 (GRCm39) |
D86G |
possibly damaging |
Het |
Echs1 |
T |
A |
7: 139,696,349 (GRCm39) |
|
probably benign |
Het |
Epha8 |
C |
T |
4: 136,663,498 (GRCm39) |
M483I |
probably benign |
Het |
Eprs1 |
T |
G |
1: 185,139,165 (GRCm39) |
V850G |
probably damaging |
Het |
Fbxw5 |
C |
A |
2: 25,392,561 (GRCm39) |
C114* |
probably null |
Het |
Gm5160 |
C |
T |
18: 14,558,129 (GRCm39) |
R69C |
probably benign |
Het |
Gpr75 |
A |
G |
11: 30,841,209 (GRCm39) |
H38R |
probably damaging |
Het |
Igsf9 |
T |
C |
1: 172,319,197 (GRCm39) |
V230A |
probably benign |
Het |
Lonp2 |
C |
T |
8: 87,435,641 (GRCm39) |
P626S |
probably damaging |
Het |
Lrrtm1 |
G |
T |
6: 77,221,095 (GRCm39) |
|
probably null |
Het |
Man1a2 |
T |
C |
3: 100,489,455 (GRCm39) |
E508G |
probably damaging |
Het |
Mipep |
C |
A |
14: 61,039,580 (GRCm39) |
A203E |
probably damaging |
Het |
Mrc1 |
T |
A |
2: 14,299,668 (GRCm39) |
C753S |
probably damaging |
Het |
Mthfr |
A |
G |
4: 148,139,467 (GRCm39) |
E568G |
probably benign |
Het |
Naca |
T |
A |
10: 127,879,479 (GRCm39) |
|
probably benign |
Het |
Nek10 |
G |
A |
14: 14,860,846 (GRCm38) |
|
probably null |
Het |
Nf2 |
T |
C |
11: 4,739,750 (GRCm39) |
T419A |
probably benign |
Het |
Npas3 |
A |
G |
12: 53,878,539 (GRCm39) |
T164A |
possibly damaging |
Het |
Nudcd3 |
T |
A |
11: 6,100,581 (GRCm39) |
I124F |
possibly damaging |
Het |
Or8g33 |
A |
G |
9: 39,337,423 (GRCm39) |
*315Q |
probably null |
Het |
Pappa2 |
A |
T |
1: 158,764,010 (GRCm39) |
C500* |
probably null |
Het |
Pcdhb18 |
T |
A |
18: 37,623,995 (GRCm39) |
S442T |
probably damaging |
Het |
Phactr4 |
T |
C |
4: 132,105,752 (GRCm39) |
N105D |
possibly damaging |
Het |
Polr1b |
C |
A |
2: 128,967,464 (GRCm39) |
F952L |
probably damaging |
Het |
Ptprb |
GAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT |
GAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT |
10: 116,119,582 (GRCm39) |
|
probably benign |
Het |
Pzp |
T |
C |
6: 128,464,496 (GRCm39) |
T1344A |
probably benign |
Het |
Ranbp9 |
T |
C |
13: 43,573,097 (GRCm39) |
I312V |
possibly damaging |
Het |
Rsf1 |
A |
G |
7: 97,310,368 (GRCm39) |
|
probably benign |
Het |
Slc6a4 |
A |
T |
11: 76,903,851 (GRCm39) |
I150L |
probably benign |
Het |
Smpd5 |
T |
C |
15: 76,180,496 (GRCm39) |
S433P |
probably benign |
Het |
Spats1 |
C |
T |
17: 45,763,644 (GRCm39) |
D209N |
probably damaging |
Het |
Spcs2 |
C |
T |
7: 99,488,984 (GRCm39) |
G235R |
probably damaging |
Het |
Synm |
T |
C |
7: 67,385,337 (GRCm39) |
D775G |
probably damaging |
Het |
Tango6 |
A |
G |
8: 107,419,245 (GRCm39) |
D264G |
probably benign |
Het |
Tbc1d30 |
A |
T |
10: 121,132,710 (GRCm39) |
L218H |
probably damaging |
Het |
Tmem132d |
A |
G |
5: 127,866,953 (GRCm39) |
I649T |
probably damaging |
Het |
Tmem145 |
T |
C |
7: 25,006,939 (GRCm39) |
Y114H |
probably damaging |
Het |
Triml1 |
A |
T |
8: 43,591,803 (GRCm39) |
V185E |
possibly damaging |
Het |
Ttll3 |
CAAAGTAA |
CAAAGTAAAGTAA |
6: 113,376,118 (GRCm39) |
|
probably null |
Het |
Ttn |
T |
G |
2: 76,715,220 (GRCm39) |
|
probably benign |
Het |
Utrn |
C |
T |
10: 12,277,050 (GRCm39) |
|
probably null |
Het |
Uty |
T |
C |
Y: 1,137,716 (GRCm39) |
K887E |
possibly damaging |
Het |
Zfand2b |
T |
C |
1: 75,145,502 (GRCm39) |
F3L |
possibly damaging |
Het |
Zfp280d |
C |
A |
9: 72,219,953 (GRCm39) |
Q243K |
possibly damaging |
Het |
Zfp418 |
T |
C |
7: 7,185,668 (GRCm39) |
F544L |
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 |
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'- AACTCTCACTAATGCTATGTCTCAC -3'
(R):5'- CACAGCCTTGACACTGTCAG -3'
Sequencing Primer
(F):5'- TCACTAATGCTATGTCTCACTATCAG -3'
(R):5'- CACAGCCTTGACACTGTCAGAATTTG -3'
|
Posted On |
2019-12-03 |