Sptlc1 MGI Mouse Gene Detail - MGI:1099431 - serine palmitoyltransferase, long chain base subunit 1

Symbol

Sptlc1
Name

serine palmitoyltransferase, long chain base subunit 1
Synonyms

Lcb1, Spt1

Feature Type

protein coding gene
IDs

MGI:1099431
NCBI Gene: 268656
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr13:53486784-53531401 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 13, 27.68 cM
Mapping Data

2 experiments

SNPs within 2kb

1111 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1099431	protein coding gene	Chr13:53486784-53531433 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0020561	protein coding gene	Chr13:52665633-52711528 (-)
A/J	MGP_AJ_G0020515	protein coding gene	Chr13:50761370-50806233 (-)
AKR/J	MGP_AKRJ_G0020493	protein coding gene	Chr13:52205318-52250047 (-)
BALB/cJ	MGP_BALBcJ_G0020511	protein coding gene	Chr13:50976812-51021667 (-)
C3H/HeJ	MGP_C3HHeJ_G0020310	protein coding gene	Chr13:52055646-52101388 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0020945	protein coding gene	Chr13:54281646-54327094 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018527	protein coding gene	Chr13:48542100-48586788 (-)
CAST/EiJ	MGP_CASTEiJ_G0019824	protein coding gene	Chr13:52073344-52119527 (-)
CBA/J	MGP_CBAJ_G0020270	protein coding gene	Chr13:56329720-56374487 (-)
DBA/2J	MGP_DBA2J_G0020393	protein coding gene	Chr13:50329948-50375372 (-)
FVB/NJ	MGP_FVBNJ_G0020372	protein coding gene	Chr13:49774270-49819762 (-)
LP/J	MGP_LPJ_G0020469	protein coding gene	Chr13:52936204-52981765 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020401	protein coding gene	Chr13:55884745-55930805 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020988	protein coding gene	Chr13:51825165-51871289 (-)
PWK/PhJ	MGP_PWKPhJ_G0019580	protein coding gene	Chr13:50282160-50327147 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0019407	protein coding gene	Chr13:50726357-50771093 (-)
WSB/EiJ	MGP_WSBEiJ_G0019886	protein coding gene	Chr13:52145111-52191731 (-)

Human Ortholog

SPTLC1, serine palmitoyltransferase long chain base subunit 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SPTLC1, serine palmitoyltransferase long chain base subunit 1
Synonyms

ALS27, HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI
Links

HGNC:11277

NCBI Gene ID: 10558

neXtProt AC: NX_O15269

UniProt: O15269
Chr Location

9q22.31; chr9:92000087-92115413 (-) GRCh38

MGI Vertebrate Homology

Sptlc1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SPTLC1
Gene Tree

Sptlc1

Diseases

2 with human SPTLC1 associations

				Human Disease	Mouse Models
				hereditary sensory and autonomic neuropathy type 1A IDs hereditary sensory and autonomic neuropathy type 1A DOID:0070152 OMIM:162400
				juvenile amyotrophic lateral sclerosis type 27 IDs juvenile amyotrophic lateral sclerosis type 27 DOID:0081381 OMIM:620285

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

9 phenotypes from 3 alleles in 3 genetic backgrounds
22 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

15
Chemically induced (other)

1
Endonuclease-mediated

7
Gene trapped

5
Targeted

2
Genomic Mutations

1 involving Sptlc1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

28 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a knock-out allele exhibit abnormal sphingolipid levels.

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All GO Annotations

28
GO References

13

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

809
Tissues

99
cDNA Data

18
Literature Summary

6

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sptlc1

ZFIN sptlc1

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All Sequences

61
RefSeq

14
UniProt

6
CCDS

CCDS26521.1

Ensembl

ENSMUSG00000021468 (Evidence)
NCBI Gene

268656

			Length	Strain/Species	Flank
genomic	268656	NCBI Gene Model \| MGI Sequence Detail	44618	C57BL/6J	± kb
transcript	NM_001426467	RefSeq \| MGI Sequence Detail	2795	C57BL/6
polypeptide	O35704	UniProt \| EBI \| MGI Sequence Detail	473	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000015596 serine palmitoyltransferase 1

(term hierarchy)
EC

2.3.1.50
InterPro Domains

IPR050087 8-amino-7-oxononanoate synthase class-II

IPR004839 Aminotransferase, class I/classII

IPR015424 Pyridoxal phosphate-dependent transferase

IPR015421 Pyridoxal phosphate-dependent transferase, major domain

IPR015422 Pyridoxal phosphate-dependent transferase, small domain

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All nucleic 22

cDNA 18

Primer pair 4

Microarray probesets 4

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MGI:2145452, MGI:2145493

Summaries

All 62

Developmental Gene Expression 6

Gene Ontology 13

Phenotypes 22
Earliest

J:182573 Roderick TH, Producing and detecting paracentric chromosomal inversions in mice. Mutat Res. 1971 Jan;11(1):59-69
Latest

J:348985 Abimannan T, et al., Sphingolipid biosynthesis is essential for metabolic rewiring during T(H)17 cell differentiation. Sci Adv. 2024 Apr 26;10(17):eadk1045

TSS for Sptlc1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr122583	Chr13:53531391-53531409 (-)	1 bp
Tssr122582	Chr13:53528343-53528355 (-)	3,052 bp
Tssr122581	Chr13:53527814-53527821 (-)	3,583 bp
Tssr122580	Chr13:53524293-53524302 (-)	7,103 bp
Tssr122579	Chr13:53523811-53523815 (-)	7,588 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24