Mutagenetix > Incidental Mutation

Incidental Mutation 'R9794:Sptlc1'

734844

Institutional Source

Beutler Lab

Gene Symbol

Sptlc1

Ensembl Gene

ENSMUSG00000021468

Gene Name

serine palmitoyltransferase, long chain base subunit 1

Synonyms

Spt1, Lcb1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9794 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

53486784-53531433 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 53512803 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 185 (I185N)

Ref Sequence

ENSEMBL: ENSMUSP00000021920 (fasta)

Gene Model

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

AlphaFold

O35704

Predicted Effect

possibly damaging
Transcript: ENSMUST00000021920
AA Change: I185N

PolyPhen 2 Score 0.932 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000021920
Gene: ENSMUSG00000021468
AA Change: I185N

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: 99.8%
10x: 99.5%
20x: 99.0%

Validation Efficiency

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930012K11Rik	T	A	14: 70,395,038 (GRCm39)	I39L	possibly damaging	Het
Acacb	T	C	5: 114,387,578 (GRCm39)	V2415A	probably benign	Het
Adgrg6	C	A	10: 14,314,196 (GRCm39)	G669C	probably damaging	Het
Ahcyl	A	G	16: 45,974,342 (GRCm39)	V345A	probably benign	Het
Arhgdib	A	G	6: 136,906,608 (GRCm39)		probably null	Het
Arhgef18	G	A	8: 3,501,634 (GRCm39)	V643I	probably benign	Het
Aspm	T	A	1: 139,406,480 (GRCm39)	I1789N	probably damaging	Het
Atm	C	T	9: 53,429,867 (GRCm39)	V390I	probably benign	Het
AW554918	A	G	18: 25,337,031 (GRCm39)	E148G	probably damaging	Het
Bmal2	T	A	6: 146,734,033 (GRCm39)	D543E	probably benign	Het
Camk2a	T	C	18: 61,097,031 (GRCm39)	V327A	probably benign	Het
Celsr3	T	C	9: 108,728,502 (GRCm39)	V3302A	probably benign	Het
Ces2a	G	A	8: 105,467,896 (GRCm39)	V509M	probably benign	Het
Cpa5	T	C	6: 30,625,920 (GRCm39)		probably null	Het
Cplx3	A	T	9: 57,509,522 (GRCm39)	*159R	probably null	Het
Cyp2b23	A	T	7: 26,381,121 (GRCm39)	Y79N	probably benign	Het
Dapk1	A	G	13: 60,909,082 (GRCm39)	T1232A	probably damaging	Het
Dsg3	A	T	18: 20,673,154 (GRCm39)	T942S	probably benign	Het
Efnb3	G	A	11: 69,448,232 (GRCm39)	P70L	probably damaging	Het
Eln	G	T	5: 134,751,352 (GRCm39)	Y280*	probably null	Het
Epha8	G	T	4: 136,666,035 (GRCm39)	H374N	probably benign	Het
Erbin	A	T	13: 103,971,359 (GRCm39)	D752E	probably benign	Het
Fam149a	A	G	8: 45,834,449 (GRCm39)	S117P	possibly damaging	Het
Fchsd2	G	A	7: 100,893,410 (GRCm39)	C304Y	probably benign	Het
Galnt6	C	A	15: 100,595,859 (GRCm39)	V390L	probably damaging	Het
Grk3	T	C	5: 113,121,448 (GRCm39)		probably null	Het
Il17rc	A	T	6: 113,453,726 (GRCm39)	T237S	probably benign	Het
Inpp5b	A	G	4: 124,687,174 (GRCm39)	D800G	probably damaging	Het
Itga11	A	G	9: 62,662,868 (GRCm39)	N528S	probably benign	Het
Kif19b	T	A	5: 140,448,070 (GRCm39)		probably null	Het
Lancl2	T	A	6: 57,714,708 (GRCm39)	F442L	probably benign	Het
Ldah	G	T	12: 8,318,430 (GRCm39)	A180S	possibly damaging	Het
Lingo1	T	C	9: 56,528,592 (GRCm39)	E5G	probably benign	Het
Lingo3	T	C	10: 80,670,707 (GRCm39)	I408V	possibly damaging	Het
Liph	A	T	16: 21,774,862 (GRCm39)	L445Q	probably damaging	Het
Lonrf1	A	G	8: 36,703,235 (GRCm39)	Y314H	probably damaging	Het
Lrit3	A	T	3: 129,594,073 (GRCm39)	L168Q	probably damaging	Het
Mideas	T	A	12: 84,220,576 (GRCm39)	Q126L	probably damaging	Het
Mylk4	G	T	13: 32,899,950 (GRCm39)	T312K	probably damaging	Het
Myzap	A	T	9: 71,487,082 (GRCm39)	M15K	probably benign	Het
Ngf	G	A	3: 102,428,132 (GRCm39)	V298M	probably damaging	Het
Nlrp9a	A	G	7: 26,264,302 (GRCm39)	I741V	probably benign	Het
Nrxn2	T	C	19: 6,567,064 (GRCm39)	V1313A	possibly damaging	Het
Nuf2	C	T	1: 169,334,954 (GRCm39)		probably null	Het
Or13a27	G	A	7: 139,925,483 (GRCm39)	Q140*	probably null	Het
Or5m8	A	G	2: 85,822,464 (GRCm39)	Y101C	probably benign	Het
Pcdh17	C	T	14: 84,770,350 (GRCm39)	R943*	probably null	Het
Phykpl	A	T	11: 51,489,212 (GRCm39)	H346L	probably benign	Het
Plk4	C	A	3: 40,759,535 (GRCm39)	L144I	probably damaging	Het
Pole	C	A	5: 110,466,201 (GRCm39)	P1301Q	probably benign	Het
Prkch	T	A	12: 73,744,744 (GRCm39)	N252K	possibly damaging	Het
Psen2	A	T	1: 180,068,294 (GRCm39)		probably null	Het
Ptgds	C	A	2: 25,359,129 (GRCm39)	R42L	probably benign	Het
Ptprz1	A	G	6: 23,000,204 (GRCm39)	T765A	probably benign	Het
Rab6b	T	C	9: 103,041,061 (GRCm39)	F152L	possibly damaging	Het
Rbm12b2	T	A	4: 12,095,335 (GRCm39)	F731L	probably damaging	Het
Resf1	T	A	6: 149,228,239 (GRCm39)	Y428*	probably null	Het
Rnf32	T	C	5: 29,429,125 (GRCm39)	I234T	probably damaging	Het
Scart2	G	A	7: 139,874,716 (GRCm39)	G398D	probably damaging	Het
Scn8a	T	A	15: 100,933,332 (GRCm39)	I1512N	probably benign	Het
Senp6	T	A	9: 79,999,590 (GRCm39)	D81E	probably benign	Het
Slc26a7	T	G	4: 14,590,416 (GRCm39)	N125T	possibly damaging	Het
Syne2	C	A	12: 76,047,617 (GRCm39)	H4013N	probably benign	Het
Tbc1d9b	T	C	11: 50,062,005 (GRCm39)	V1171A	probably benign	Het
Tmem63b	T	C	17: 45,977,252 (GRCm39)	N417S	probably benign	Het
Ttn	A	G	2: 76,706,193 (GRCm39)	V9176A	unknown	Het
Vmn1r210	T	C	13: 23,011,432 (GRCm39)	I285V	probably damaging	Het
Wbp11	C	T	6: 136,795,021 (GRCm39)	V308I	possibly damaging	Het
Wnk2	A	C	13: 49,229,674 (GRCm39)	V950G	probably benign	Het
Zfp110	A	G	7: 12,578,521 (GRCm39)	N144S	probably benign	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
R6415:Sptlc1	UTSW	13	53,505,728 (GRCm39)	critical splice acceptor site	probably null
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

Predicted Primers

PCR Primer
(F):5'- AGGGTCTTGACCAGGAAAAC -3'
(R):5'- CCATTTTGTCTGTAAGGTGAAAGG -3'

Sequencing Primer
(F):5'- GTCTTGACCAGGAAAACAAGCAAAAC -3'
(R):5'- GGGGCAGTAATTAAATGACTATGTAC -3'

Posted On

2022-11-14