Incidental Mutation 'R3417:Sptlc2'
| ID |
266859 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sptlc2
|
| Ensembl Gene |
ENSMUSG00000021036 |
| Gene Name |
serine palmitoyltransferase, long chain base subunit 2 |
| Synonyms |
LCB2, Spt2 |
| MMRRC Submission |
040635-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3417 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
87351832-87435129 bp(-) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to G
at 87393582 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021424
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021424]
|
| AlphaFold |
P97363 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021424
|
| SMART Domains |
Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Aminotran_1_2
|
166 |
526 |
7.2e-60 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167911
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169845
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170110
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.7%
|
| Validation Efficiency |
98% (54/55) |
| MGI Phenotype |
FUNCTION: This gene encodes a long chain base subunit of serine palmitoyltransferase. The enzyme, serine palmitoyltransferase, consists of two different subunits, and is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. A mutant allele of this gene in mice is used as a model for the human disease 'Susceptibilty to Psoriasis 1'. Mutations in the human gene are associated with hereditary sensory neuropathy type I. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice heterozygous for this allele exhibit abnormal liver and circulating shingolipid levels. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc5 |
A |
G |
16: 20,224,302 (GRCm39) |
|
probably benign |
Het |
| Adgrl2 |
T |
C |
3: 148,564,965 (GRCm39) |
Y201C |
probably damaging |
Het |
| Ankar |
A |
G |
1: 72,698,135 (GRCm39) |
|
probably null |
Het |
| Ankrd17 |
G |
A |
5: 90,391,772 (GRCm39) |
T1857I |
possibly damaging |
Het |
| Atp6v0d2 |
A |
G |
4: 19,888,829 (GRCm39) |
|
probably benign |
Het |
| Cep170 |
G |
T |
1: 176,583,610 (GRCm39) |
P923Q |
probably damaging |
Het |
| Cfc1 |
A |
T |
1: 34,575,457 (GRCm39) |
R44* |
probably null |
Het |
| Col6a1 |
C |
T |
10: 76,548,203 (GRCm39) |
V618M |
unknown |
Het |
| Crmp1 |
A |
T |
5: 37,426,031 (GRCm39) |
I159L |
possibly damaging |
Het |
| Crocc |
G |
A |
4: 140,773,758 (GRCm39) |
T103I |
possibly damaging |
Het |
| Cyp4f39 |
T |
C |
17: 32,708,716 (GRCm39) |
V421A |
possibly damaging |
Het |
| Ero1a |
T |
C |
14: 45,525,323 (GRCm39) |
T401A |
possibly damaging |
Het |
| Exoc6b |
C |
G |
6: 84,867,547 (GRCm39) |
L288F |
possibly damaging |
Het |
| Fsip2 |
G |
A |
2: 82,816,854 (GRCm39) |
V4196I |
possibly damaging |
Het |
| Icosl |
A |
T |
10: 77,907,869 (GRCm39) |
N143I |
possibly damaging |
Het |
| Igsf9b |
G |
A |
9: 27,220,774 (GRCm39) |
V47I |
possibly damaging |
Het |
| Irag1 |
T |
C |
7: 110,476,161 (GRCm39) |
T597A |
possibly damaging |
Het |
| Jrk |
A |
G |
15: 74,578,734 (GRCm39) |
Y184H |
probably damaging |
Het |
| Kdm5b |
T |
C |
1: 134,515,715 (GRCm39) |
L113P |
probably damaging |
Het |
| Klhl42 |
G |
A |
6: 147,009,378 (GRCm39) |
V406M |
probably damaging |
Het |
| Lrp12 |
A |
G |
15: 39,741,678 (GRCm39) |
F365L |
probably damaging |
Het |
| Lrrc37 |
A |
T |
11: 103,505,435 (GRCm39) |
S2178T |
possibly damaging |
Het |
| Map4k5 |
A |
T |
12: 69,856,038 (GRCm39) |
V716E |
probably damaging |
Het |
| Mcm9 |
T |
C |
10: 53,413,503 (GRCm39) |
T1264A |
possibly damaging |
Het |
| Mia3 |
T |
A |
1: 183,143,444 (GRCm39) |
D100V |
probably damaging |
Het |
| Mrgprb2 |
C |
A |
7: 48,202,281 (GRCm39) |
R148L |
probably damaging |
Het |
| Mterf1a |
A |
G |
5: 3,940,795 (GRCm39) |
S358P |
probably damaging |
Het |
| Myd88 |
T |
C |
9: 119,166,556 (GRCm39) |
I253V |
possibly damaging |
Het |
| Naip6 |
C |
T |
13: 100,437,108 (GRCm39) |
A472T |
probably benign |
Het |
| Nqo2 |
G |
T |
13: 34,163,616 (GRCm39) |
V92L |
probably benign |
Het |
| Or4k2 |
T |
A |
14: 50,424,069 (GRCm39) |
T202S |
possibly damaging |
Het |
| Pcdhb15 |
A |
T |
18: 37,608,216 (GRCm39) |
N483Y |
probably damaging |
Het |
| Pds5a |
A |
G |
5: 65,795,235 (GRCm39) |
F667S |
probably damaging |
Het |
| Plxnb1 |
C |
A |
9: 108,929,828 (GRCm39) |
A228E |
probably damaging |
Het |
| Prpsap1 |
T |
C |
11: 116,369,410 (GRCm39) |
S179G |
probably benign |
Het |
| Rtl4 |
C |
T |
X: 143,902,901 (GRCm39) |
Q108* |
probably null |
Het |
| Scn8a |
A |
G |
15: 100,869,549 (GRCm39) |
|
probably benign |
Het |
| Sla2 |
G |
A |
2: 156,717,862 (GRCm39) |
R137C |
probably damaging |
Het |
| Slc44a1 |
G |
A |
4: 53,553,549 (GRCm39) |
V519I |
probably benign |
Het |
| Smg1 |
G |
C |
7: 117,748,076 (GRCm39) |
|
probably benign |
Het |
| St13 |
A |
T |
15: 81,253,651 (GRCm39) |
|
probably benign |
Het |
| Strbp |
C |
G |
2: 37,480,737 (GRCm39) |
R610T |
possibly damaging |
Het |
| Tas2r124 |
A |
T |
6: 132,732,601 (GRCm39) |
R303S |
probably benign |
Het |
| Tex55 |
A |
C |
16: 38,649,102 (GRCm39) |
D2E |
probably benign |
Het |
| Tgm3 |
G |
A |
2: 129,889,692 (GRCm39) |
V629M |
possibly damaging |
Het |
| Tnr |
T |
C |
1: 159,722,612 (GRCm39) |
V1019A |
probably benign |
Het |
| Ttn |
A |
T |
2: 76,615,908 (GRCm39) |
C14932* |
probably null |
Het |
| Vrk3 |
C |
T |
7: 44,424,866 (GRCm39) |
T427M |
probably benign |
Het |
|
| Other mutations in Sptlc2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00757:Sptlc2
|
APN |
12 |
87,415,842 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02458:Sptlc2
|
APN |
12 |
87,356,667 (GRCm39) |
utr 3 prime |
probably benign |
|
|
IGL02734:Sptlc2
|
APN |
12 |
87,402,444 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL03252:Sptlc2
|
APN |
12 |
87,402,431 (GRCm39) |
missense |
probably benign |
0.00 |
|
lopsided
|
UTSW |
12 |
87,388,339 (GRCm39) |
missense |
probably benign |
0.27 |
|
shinola
|
UTSW |
12 |
87,397,069 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R0087:Sptlc2
|
UTSW |
12 |
87,415,892 (GRCm39) |
missense |
probably benign |
|
|
R0116:Sptlc2
|
UTSW |
12 |
87,403,454 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0492:Sptlc2
|
UTSW |
12 |
87,393,580 (GRCm39) |
splice site |
probably null |
|
|
R1353:Sptlc2
|
UTSW |
12 |
87,388,520 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1470:Sptlc2
|
UTSW |
12 |
87,402,414 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1470:Sptlc2
|
UTSW |
12 |
87,402,414 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3735:Sptlc2
|
UTSW |
12 |
87,388,339 (GRCm39) |
missense |
probably benign |
0.27 |
|
R3736:Sptlc2
|
UTSW |
12 |
87,388,339 (GRCm39) |
missense |
probably benign |
0.27 |
|
R4278:Sptlc2
|
UTSW |
12 |
87,382,925 (GRCm39) |
missense |
probably benign |
0.04 |
|
R5252:Sptlc2
|
UTSW |
12 |
87,382,829 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R5593:Sptlc2
|
UTSW |
12 |
87,415,857 (GRCm39) |
missense |
probably benign |
0.11 |
|
R5656:Sptlc2
|
UTSW |
12 |
87,393,535 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5801:Sptlc2
|
UTSW |
12 |
87,388,545 (GRCm39) |
splice site |
probably null |
|
|
R6256:Sptlc2
|
UTSW |
12 |
87,402,305 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6280:Sptlc2
|
UTSW |
12 |
87,434,905 (GRCm39) |
missense |
probably benign |
|
|
R6520:Sptlc2
|
UTSW |
12 |
87,402,436 (GRCm39) |
missense |
probably benign |
|
|
R6808:Sptlc2
|
UTSW |
12 |
87,397,069 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R7133:Sptlc2
|
UTSW |
12 |
87,397,151 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7274:Sptlc2
|
UTSW |
12 |
87,388,380 (GRCm39) |
missense |
probably benign |
0.24 |
|
R7366:Sptlc2
|
UTSW |
12 |
87,360,823 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7602:Sptlc2
|
UTSW |
12 |
87,388,463 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9085:Sptlc2
|
UTSW |
12 |
87,382,839 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9710:Sptlc2
|
UTSW |
12 |
87,359,533 (GRCm39) |
missense |
probably benign |
0.44 |
|
Z1177:Sptlc2
|
UTSW |
12 |
87,415,818 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- CTTACGTAATCACTAACACTGTCC -3'
(R):5'- AGCACCATTTCTACAGCTGCC -3'
Sequencing Primer
(F):5'- ATCACTAACACTGTCCAAAGAATATC -3'
(R):5'- ACAGCTGCCCTTTCTCAAAAATTG -3'
|
| Posted On |
2015-02-18 |
Incidental Mutation