Gene Report

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Basic Info

Approved Symbol	SPTLC1
Previous Symbol	HSN1
Symbol Alias	LCB1, SPTI, HSAN1, hLCB1
Approved Name	serine palmitoyltransferase, long chain base subunit 1
Previous Name	hereditary sensory neuropathy, type 1
Location	9q22.31
Position	chr9:92031999-92115384, -1
External Links	HGNC: 11277 Entrez Gene: 10558 Ensembl: ENSG00000090054 UCSC: uc011ltv.2
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Bergen, S. E.,2012	SNP: rs7872515	No significant association was observed in BD.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 14)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016021	integral component of membrane	cellular component	IEA	219

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0006665	sphingolipid metabolic process	biological process	TAS	6
GO:0046513	ceramide biosynthetic process	biological process	IEA	3
GO:0035339	SPOTS complex	cellular component	IDA[20182505]	1
GO:0017059	serine C-palmitoyltransferase complex	cellular component	IDA[19416851]	1
GO:0030148	sphingolipid biosynthetic process	biological process	TAS[19416851]	3
GO:0005515	protein binding	molecular function	IPI[19416851]	563
GO:0046511	sphinganine biosynthetic process	biological process	IEA	1
GO:0046512	sphingosine biosynthetic process	biological process	IEA	1
GO:0004758	serine C-palmitoyltransferase activity	molecular function	IDA[19416851]	1
GO:0005789	endoplasmic reticulum membrane	cellular component	TAS	52
GO:0030170	pyridoxal phosphate binding	molecular function	IEA	5
GO:0006686	sphingomyelin biosynthetic process	biological process	IEA	1
GO:0044281	small molecule metabolic process	biological process	TAS	117

Gene related KEGG pathways (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa00600	Sphingolipid metabolism	1

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
SPTLC1	ABCA1	YES	in vivo	18484747
SPTLC1	SPTLC2	NO	in vitro;in vivo	10722674

Related other genetic factors

Gene related SNPs (count: 14)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs7872515	chr9:92060258 - 92060258(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)

rs_ID	Location	Functional Annotation
rs1970121	chr9:92107870 - 92107870(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs10992234	chr9:92115554 - 92115554(1)	downstream_gene_variant; upstream_gene_variant
rs7872238	chr9:92029937 - 92029937(1)	downstream_gene_variant
rs10123181	chr9:92030049 - 92030049(1)	downstream_gene_variant
rs16908106	chr9:92036571 - 92036571(1)	intron_variant; non_coding_transcript_variant
rs7852067	chr9:92053312 - 92053312(1)	intron_variant
rs7858659	chr9:92059864 - 92059864(1)	intron_variant; non_coding_transcript_variant
rs7860518	chr9:92064183 - 92064183(1)	intron_variant; non_coding_transcript_variant
rs10820936	chr9:92068692 - 92068692(1)	intron_variant; non_coding_transcript_variant
rs10992221	chr9:92069761 - 92069761(1)	intron_variant; non_coding_transcript_variant
rs7856177	chr9:92077060 - 92077060(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs10820937	chr9:92077924 - 92077924(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7029539	chr9:92102040 - 92102040(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
9q21-32	chr9:65000000-114900000	1 (0/1/0)
Chr 9	chr9:0-138394717	3 (0/3/0)
9q21-22	chr9:65000000-99800000	1 (0/1/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Reference	Description	Result Category
22688191	No significant association was observed in SZ.	Negative

Gene relationship with MDD

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Region: chr9:92031999..92115384 View in gBrowse