Mutagenetix > Incidental Mutation

Incidental Mutation 'R6280:Sptlc2'

531222

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2, Spt2

MMRRC Submission

044450-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6280 (G1)

Quality Score

75.0075

Status

Validated

Chromosome

Chromosomal Location

87351832-87435129 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 87434905 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 14 (M14K)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021424]

AlphaFold

P97363

Predicted Effect

probably benign
Transcript: ENSMUST00000021424
AA Change: M14K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: M14K

Domain	Start	End	E-Value	Type
Pfam:Aminotran_1_2	166	526	7.2e-60	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

100% (75/75)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	C	T	1: 71,311,619 (GRCm39)	D1930N	probably benign	Het
Adam8	A	G	7: 139,564,720 (GRCm39)	L667S	probably damaging	Het
Adcy4	A	T	14: 56,016,500 (GRCm39)	I317N	probably damaging	Het
Agpat3	A	G	10: 78,120,872 (GRCm39)	F102S	probably damaging	Het
Apbb2	A	T	5: 66,522,325 (GRCm39)	W443R	probably damaging	Het
BC049715	T	A	6: 136,817,229 (GRCm39)	Y156*	probably null	Het
Bpifc	C	T	10: 85,813,576 (GRCm39)	V323I	probably benign	Het
Camp	T	G	9: 109,676,577 (GRCm39)	I149L	probably benign	Het
Cfap20dc	T	G	14: 8,473,414 (GRCm38)		probably null	Het
Cibar2	A	G	8: 120,898,858 (GRCm39)	I94T	possibly damaging	Het
Cnih1	A	G	14: 47,025,634 (GRCm39)		probably null	Het
Col18a1	A	T	10: 76,948,323 (GRCm39)		probably benign	Het
Dsg4	A	T	18: 20,599,724 (GRCm39)	D780V	probably damaging	Het
Dync1i1	G	A	6: 5,972,084 (GRCm39)	V442I	probably benign	Het
Fam83g	G	T	11: 61,594,008 (GRCm39)	S514I	probably benign	Het
Fbxo7	A	G	10: 85,864,969 (GRCm39)	N93D	probably benign	Het
Fgf20	G	T	8: 40,734,153 (GRCm39)	S76*	probably null	Het
Foxi1	A	G	11: 34,157,972 (GRCm39)	F18L	probably damaging	Het
Fxr1	G	A	3: 34,100,401 (GRCm39)		probably benign	Het
Gon4l	T	A	3: 88,798,195 (GRCm39)	L800H	probably damaging	Het
Gpn3	T	A	5: 122,512,022 (GRCm39)	S33T	probably benign	Het
Gria4	T	C	9: 4,456,072 (GRCm39)	M743V	probably damaging	Het
Hira	A	G	16: 18,729,457 (GRCm39)	N109D	probably damaging	Het
Hsd3b3	A	G	3: 98,660,621 (GRCm39)		probably null	Het
Hsf2	T	G	10: 57,387,591 (GRCm39)	S370A	probably benign	Het
Htt	T	A	5: 35,028,103 (GRCm39)	D1786E	probably benign	Het
Ifit1bl2	T	A	19: 34,597,534 (GRCm39)	R27S	possibly damaging	Het
Il17rb	G	A	14: 29,724,928 (GRCm39)	A186V	probably benign	Het
Irak4	G	T	15: 94,449,691 (GRCm39)	E57*	probably null	Het
Kcnh2	T	A	5: 24,536,921 (GRCm39)	H221L	probably benign	Het
Kdm2b	T	C	5: 123,016,687 (GRCm39)	N1149D	probably damaging	Het
Kif26a	A	G	12: 112,141,303 (GRCm39)	H702R	probably damaging	Het
Kmt2e	T	C	5: 23,704,514 (GRCm39)	S1236P	possibly damaging	Het
Krt77	T	A	15: 101,773,910 (GRCm39)	D248V	probably damaging	Het
Lgals3bp	T	C	11: 118,284,106 (GRCm39)	N52S	possibly damaging	Het
Lhfpl6	T	C	3: 53,167,935 (GRCm39)	Y170H	probably damaging	Het
Lpin2	A	G	17: 71,539,243 (GRCm39)		probably benign	Het
Lrig3	T	C	10: 125,846,848 (GRCm39)	I872T	probably benign	Het
Lrit3	T	C	3: 129,582,412 (GRCm39)	E525G	probably damaging	Het
Lrp1	T	C	10: 127,425,453 (GRCm39)	T726A	probably benign	Het
Mep1a	A	T	17: 43,813,283 (GRCm39)	N46K	probably damaging	Het
Muc16	C	A	9: 18,490,613 (GRCm39)		probably null	Het
N4bp1	A	C	8: 87,579,794 (GRCm39)	N669K	possibly damaging	Het
Nelfcd	A	G	2: 174,257,739 (GRCm39)	D26G	probably benign	Het
Neu4	G	A	1: 93,952,873 (GRCm39)	S414N	probably damaging	Het
Nudt9	A	G	5: 104,212,935 (GRCm39)	D336G	probably benign	Het
Obscn	C	A	11: 58,954,509 (GRCm39)	G3691V	possibly damaging	Het
Or4c52	A	C	2: 89,845,393 (GRCm39)	I40L	possibly damaging	Het
Or5t17	A	G	2: 86,832,364 (GRCm39)	N17S	probably damaging	Het
Pdgfd	T	A	9: 6,288,627 (GRCm39)	S94T	probably benign	Het
Picalm	A	G	7: 89,826,770 (GRCm39)	H290R	probably benign	Het
Pou2f3	A	T	9: 43,050,634 (GRCm39)	L242Q	probably damaging	Het
Pou2f3	G	T	9: 43,050,635 (GRCm39)	L242M	probably damaging	Het
Prkd3	C	T	17: 79,289,360 (GRCm39)	G187D	probably damaging	Het
Pwp1	A	G	10: 85,710,326 (GRCm39)	S49G	probably damaging	Het
Ralgapa2	A	G	2: 146,184,129 (GRCm39)	L1626P	probably damaging	Het
Resf1	T	C	6: 149,228,555 (GRCm39)	S534P	probably damaging	Het
Rin2	A	G	2: 145,702,939 (GRCm39)	Y545C	probably damaging	Het
Rwdd4a	A	G	8: 47,995,832 (GRCm39)	T71A	probably benign	Het
Senp7	T	C	16: 55,982,738 (GRCm39)	F504L	possibly damaging	Het
Slc12a6	A	G	2: 112,167,703 (GRCm39)	T231A	probably damaging	Het
Slc13a2	CGTTATCTGT	CGT	11: 78,294,306 (GRCm39)		probably benign	Het
Slc34a1	A	G	13: 24,006,377 (GRCm39)	S468G	probably benign	Het
Slc4a10	A	G	2: 62,112,310 (GRCm39)	N697S	probably benign	Het
Spint1	T	A	2: 119,075,759 (GRCm39)	V194E	possibly damaging	Het
Stard9	A	G	2: 120,531,608 (GRCm39)	K2622E	probably benign	Het
Tbc1d5	T	C	17: 51,089,338 (GRCm39)	N614S	probably benign	Het
Tdpoz2	A	T	3: 93,559,190 (GRCm39)	C261S	probably benign	Het
Tmem150b	A	T	7: 4,727,373 (GRCm39)	I44N	probably benign	Het
Ttn	A	G	2: 76,608,502 (GRCm39)	L17807P	probably damaging	Het
Vcan	G	A	13: 89,873,492 (GRCm39)	R121W	probably damaging	Het
Vmn2r15	T	A	5: 109,441,291 (GRCm39)	H189L	possibly damaging	Het
Vmn2r19	A	G	6: 123,313,212 (GRCm39)	S761G	probably benign	Het
Wdr11	A	T	7: 129,200,830 (GRCm39)	K34*	probably null	Het
Zfp120	A	T	2: 149,959,964 (GRCm39)	S141R	possibly damaging	Het
Zfp462	C	G	4: 55,010,253 (GRCm39)	P740A	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
R3417:Sptlc2	UTSW	12	87,393,582 (GRCm39)	splice site	probably benign
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
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'- ATAGTTGTAGAGTCCCGCGC -3'
(R):5'- GGTCAATAGCCGATAGACCC -3'

Sequencing Primer
(F):5'- TCAGCACACCTGAGCCG -3'
(R):5'- GATAGACCCCGCCCCATGTTC -3'

Posted On

2018-08-06