Mutagenetix > Incidental Mutation

Incidental Mutation 'R6415:Sptlc1'

517889

Institutional Source

Beutler Lab

Gene Symbol

Sptlc1

Ensembl Gene

ENSMUSG00000021468

Gene Name

serine palmitoyltransferase, long chain base subunit 1

Synonyms

Spt1, Lcb1

MMRRC Submission

044557-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6415 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

53486784-53531433 bp(-) (GRCm39)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

T to C at 53505728 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000021920 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021920]

AlphaFold

O35704

Predicted Effect

probably null
Transcript: ENSMUST00000021920

SMART Domains

Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468

Domain	Start	End	E-Value	Type
transmembrane domain	20	40	N/A	INTRINSIC
Pfam:Aminotran_1_2	98	464	9.5e-44	PFAM

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.8%
20x: 93.1%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a knock-out allele exhibit abnormal sphingolipid levels. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	G	A	9: 55,881,296 (GRCm39)	T482M	probably benign	Het
Adam9	A	G	8: 25,468,498 (GRCm39)	Y513H	probably damaging	Het
Adamts20	C	T	15: 94,222,540 (GRCm39)		probably null	Het
B3gnt5	A	G	16: 19,588,759 (GRCm39)	D326G	probably damaging	Het
Cacna1g	A	G	11: 94,354,243 (GRCm39)	I224T	probably damaging	Het
Ccdc18	A	G	5: 108,309,612 (GRCm39)	I402M	probably benign	Het
Cckar	A	T	5: 53,860,398 (GRCm39)	C73S	probably damaging	Het
Cdk13	C	T	13: 17,913,739 (GRCm39)	R880H	probably damaging	Het
Col1a1	A	G	11: 94,830,986 (GRCm39)	N218D	unknown	Het
Csnk1g2	T	C	10: 80,474,130 (GRCm39)	I145T	possibly damaging	Het
Cul5	T	C	9: 53,557,983 (GRCm39)	D207G	probably benign	Het
Cyp2c69	A	G	19: 39,831,365 (GRCm39)	F483L	probably benign	Het
Ddx60	A	G	8: 62,436,939 (GRCm39)	D963G	probably benign	Het
Dhx8	G	T	11: 101,628,513 (GRCm39)	A142S	unknown	Het
Dock7	C	T	4: 98,880,685 (GRCm39)	R926Q	probably damaging	Het
Dscaml1	C	T	9: 45,594,975 (GRCm39)	Q693*	probably null	Het
Dysf	G	A	6: 84,117,024 (GRCm39)	C1234Y	probably damaging	Het
Ercc1	G	A	7: 19,089,102 (GRCm39)		probably null	Het
Fam91a1	T	C	15: 58,314,766 (GRCm39)	L549P	probably damaging	Het
Fxyd2	T	A	9: 45,314,592 (GRCm39)	Y5N	possibly damaging	Het
Gab1	C	A	8: 81,515,226 (GRCm39)	R364L	possibly damaging	Het
Gpr182	T	A	10: 127,586,375 (GRCm39)	D192V	possibly damaging	Het
Gps1	T	C	11: 120,678,548 (GRCm39)	V286A	possibly damaging	Het
Grk1	A	G	8: 13,463,127 (GRCm39)	Y383C	probably damaging	Het
H2bc15	T	C	13: 21,938,656 (GRCm39)	Y122H	probably benign	Het
Hic1	G	A	11: 75,057,143 (GRCm39)	P582L	possibly damaging	Het
Igkv4-61	C	A	6: 69,394,138 (GRCm39)	A31S	possibly damaging	Het
Khdc4	T	C	3: 88,607,279 (GRCm39)	F328L	probably benign	Het
Lactb	T	C	9: 66,877,927 (GRCm39)	K301E	possibly damaging	Het
Lrp3	A	T	7: 34,903,593 (GRCm39)	V251E	probably benign	Het
Mapt	G	A	11: 104,189,824 (GRCm39)	G265S	probably benign	Het
Obscn	A	T	11: 58,925,956 (GRCm39)	D6245E	probably damaging	Het
Or10al2	G	T	17: 37,983,448 (GRCm39)	C178F	possibly damaging	Het
Or1j12	A	G	2: 36,342,617 (GRCm39)	S7G	probably damaging	Het
Or4b1c	T	A	2: 90,126,381 (GRCm39)	I275F	probably damaging	Het
Or4c10b	T	C	2: 89,711,206 (GRCm39)	L12P	probably damaging	Het
Or6c207	T	C	10: 129,104,890 (GRCm39)	T101A	probably benign	Het
Or7e165	T	A	9: 19,695,044 (GRCm39)	I205N	probably damaging	Het
Or7g19	T	C	9: 18,856,415 (GRCm39)	L157P	probably damaging	Het
Oxsm	A	T	14: 16,241,904 (GRCm38)	H288Q	probably benign	Het
Pcdh9	C	T	14: 93,253,278 (GRCm39)	M1128I	possibly damaging	Het
Pcdha8	T	C	18: 37,127,614 (GRCm39)	Y699H	probably damaging	Het
Pgk2	A	T	17: 40,518,459 (GRCm39)	I323N	probably benign	Het
Plin4	A	G	17: 56,410,264 (GRCm39)	V1216A	probably damaging	Het
Ppargc1a	T	C	5: 51,620,176 (GRCm39)		probably benign	Het
Prelp	A	T	1: 133,840,516 (GRCm39)	I322N	probably benign	Het
Prelp	A	T	1: 133,842,395 (GRCm39)	I250N	probably damaging	Het
Prss27	T	A	17: 24,261,882 (GRCm39)	C63*	probably null	Het
Rab38	G	A	7: 88,079,748 (GRCm39)	A47T	possibly damaging	Het
Rprd2	G	A	3: 95,681,531 (GRCm39)	A436V	probably benign	Het
Sacs	A	T	14: 61,442,808 (GRCm39)	N1618I	probably damaging	Het
Scp2	T	G	4: 107,962,337 (GRCm39)	S63R	probably benign	Het
Sftpb	T	G	6: 72,281,633 (GRCm39)	W9G	probably damaging	Het
Slco1a4	A	T	6: 141,780,415 (GRCm39)	L125*	probably null	Het
Sub1	T	A	15: 11,986,560 (GRCm39)	M96L	probably benign	Het
Tanc1	T	C	2: 59,667,458 (GRCm39)	V1233A	probably benign	Het
Tmem140	A	T	6: 34,849,658 (GRCm39)	D58V	probably damaging	Het
Tmem231	G	A	8: 112,653,524 (GRCm39)		probably benign	Het
Tpt1	T	C	14: 76,083,811 (GRCm39)	Y91H	probably benign	Het
Trap1	C	T	16: 3,861,856 (GRCm39)	R636H	possibly damaging	Het
Ttc14	A	G	3: 33,857,724 (GRCm39)	H275R	possibly damaging	Het
Tut7	T	A	13: 59,964,110 (GRCm39)		probably null	Het
Vps35l	T	C	7: 118,391,869 (GRCm39)	W494R	probably damaging	Het
Ypel1	A	G	16: 16,921,438 (GRCm39)		probably null	Het
Zbtb44	T	A	9: 30,975,510 (GRCm39)	I380N	possibly damaging	Het
Zswim5	T	C	4: 116,838,063 (GRCm39)	F798L	possibly damaging	Het

Other mutations in Sptlc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00811:Sptlc1	APN	13	53,521,414 (GRCm39)	missense	probably damaging	0.98
IGL01354:Sptlc1	APN	13	53,487,987 (GRCm39)	missense	probably benign
IGL01773:Sptlc1	APN	13	53,531,334 (GRCm39)	missense	probably damaging	0.96
IGL01876:Sptlc1	APN	13	53,528,048 (GRCm39)	missense	probably benign	0.02
R0390:Sptlc1	UTSW	13	53,491,648 (GRCm39)	missense	probably benign	0.06
R1371:Sptlc1	UTSW	13	53,505,660 (GRCm39)	missense	probably benign
R1961:Sptlc1	UTSW	13	53,512,916 (GRCm39)	missense	probably benign
R2179:Sptlc1	UTSW	13	53,505,675 (GRCm39)	missense	probably damaging	1.00
R2513:Sptlc1	UTSW	13	53,491,676 (GRCm39)	missense	possibly damaging	0.61
R4357:Sptlc1	UTSW	13	53,528,068 (GRCm39)	missense	probably damaging	1.00
R4989:Sptlc1	UTSW	13	53,505,692 (GRCm39)	missense	probably damaging	0.97
R5055:Sptlc1	UTSW	13	53,496,218 (GRCm39)	missense	probably benign	0.02
R6752:Sptlc1	UTSW	13	53,489,394 (GRCm39)	missense	possibly damaging	0.67
R7283:Sptlc1	UTSW	13	53,498,914 (GRCm39)	missense	probably benign	0.03
R7548:Sptlc1	UTSW	13	53,521,968 (GRCm39)	missense	possibly damaging	0.84
R7731:Sptlc1	UTSW	13	53,487,993 (GRCm39)	missense	probably benign	0.00
R9268:Sptlc1	UTSW	13	53,512,872 (GRCm39)	missense	probably damaging	1.00
R9302:Sptlc1	UTSW	13	53,528,047 (GRCm39)	missense	probably benign	0.06
R9794:Sptlc1	UTSW	13	53,512,803 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- GAGGTCAGACTTGCCACAAG -3'
(R):5'- AACTGCCTAAGAGTGAACGG -3'

Sequencing Primer
(F):5'- CTACAGCACCAGCCTGTG -3'
(R):5'- GAGTGAACGGAAACTGCTTTTTCTC -3'

Posted On

2018-05-24