CERS3 ceramide synthase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CERS3provided by HGNC
Official Full Name: ceramide synthase 3provided by HGNC
Primary source: HGNC:HGNC:23752
See related: Ensembl:ENSG00000154227 MIM:615276; AllianceGenome:HGNC:23752
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ARCI9; LASS3
Summary: This gene is a member of the ceramide synthase family of genes. The ceramide synthase enzymes regulate sphingolipid synthesis by catalyzing the formation of ceramides from sphingoid base and acyl-coA substrates. This family member is involved in the synthesis of ceramides with ultra-long-chain acyl moieties (ULC-Cers), important to the epidermis in its role in creating a protective barrier from the environment. The protein encoded by this gene has also been implicated in modification of the lipid structures required for spermatogenesis. Mutations in this gene have been associated with male fertility defects, and epidermal defects, including ichthyosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
Expression: Biased expression in skin (RPKM 15.5), esophagus (RPKM 13.5) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 15q26.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (100400395..100544683, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (98159133..98303123, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (100940600..101084888, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel homozygous splice site variant in CERS3 causes autosomal recessive congenital ichthyosis.
Title: A novel homozygous splice site variant in CERS3 causes autosomal recessive congenital ichthyosis.
Ceramide synthase 3 affects invasion and metastasis of hepatocellular carcinoma via the SMAD6 gene.", trans "3SMAD6.
Title: Ceramide synthase 3 affects invasion and metastasis of hepatocellular carcinoma via the SMAD6 gene.
beta-Sitosterol 3-O-D-glucoside increases ceramide levels in the stratum corneum via the up-regulated expression of ceramide synthase-3 and glucosylceramide synthase in a reconstructed human epidermal keratinization model.
Title: β-Sitosterol 3-O-D-glucoside increases ceramide levels in the stratum corneum via the up-regulated expression of ceramide synthase-3 and glucosylceramide synthase in a reconstructed human epidermal keratinization model.
Congenital ichthyosis in Prader-Willi syndrome associated with maternal chromosome 15 uniparental disomy: Case report and review of autosomal recessive conditions unmasked by UPD.
Title: Congenital ichthyosis in Prader-Willi syndrome associated with maternal chromosome 15 uniparental disomy: Case report and review of autosomal recessive conditions unmasked by UPD.
Activation of SIRT1 Enhances Epidermal Permeability Barrier Formation through Ceramide Synthase 2- and 3-Dependent Mechanisms.
Title: Activation of SIRT1 Enhances Epidermal Permeability Barrier Formation through Ceramide Synthase 2- and 3-Dependent Mechanisms.
Novel mutations in CERS3 co-segregated with the ichthyosis phenotype in six Iranian families.
Title: Autosomal recessive congenital ichthyosis: CERS3 mutations identified by a next generation sequencing panel targeting ichthyosis genes.
These results suggest that the phosphorylation of ceramide synthases may be a key regulatory point in the control of the distribution and levels of sphingolipids of various acyl-chain lengths.
Title: Enzyme Activities of the Ceramide Synthases CERS2-6 Are Regulated by Phosphorylation in the C-terminal Region.
testis-specific SLs, which we also link to CerS3 in human testis, are quintessential for male fertility.
Title: Male meiotic cytokinesis requires ceramide synthase 3-dependent sphingolipids with unique membrane anchors.
Our findings demonstrate that synthesis of very long chain ceramides by CerS3 is a crucial early step for the skin barrier formation and link disorders presenting with congenital ichthyosis to defects in sphingolipid metabolism and lipid architecture.
Title: Impaired epidermal ceramide synthesis causes autosomal recessive congenital ichthyosis and reveals the importance of ceramide acyl chain length.
these data present a novel pathway involved in ARCI development and, moreover, provide the first evidence that CERS3 plays an essential role in human sphingolipid metabolism for the maintenance of epidermal lipid homeostasis.
Title: Mutations in CERS3 cause autosomal recessive congenital ichthyosis in humans.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive congenital ichthyosis 9 MedGen: C3554349 OMIM: 615023 GeneReviews: Autosomal Recessive Congenital Ichthyosis	Compare labs

EBI GWAS Catalog

Description
The Contribution of Common Genetic Variation to Nicotine and Cotinine Glucuronidation in Multiple Ethnic/Racial Populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates the expression of ceramide synthase 3 (CERS3) in human primary T cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-79062 (e-PCR)
- UniSTS:100937

SHGC-144879 (e-PCR)
- UniSTS:172471

D13S1236 (e-PCR), detects polymorphism
- UniSTS:47290

RH92119 (e-PCR)
- UniSTS:85723

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sphingosine N-acyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables sphingosine N-acyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables sphingosine N-acyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in ceramide biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ceramide biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ceramide biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cornification	ISS Inferred from Sequence or Structural Similarity more info
involved_in epidermis development	ISS Inferred from Sequence or Structural Similarity more info
involved_in keratinocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingolipid biosynthetic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: ceramide synthase 3

Names: LAG1 homolog, ceramide synthase 3; LAG1 longevity assurance homolog 3; dihydroceramide synthase 3; sphingosine N-acyltransferase CERS3; ultra-long-chain ceramide synthase CERS3; very-long-chain ceramide synthase CERS3

NP_001277270.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

NP_001277271.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

NP_001277272.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

NP_001365718.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

NP_849164.2

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_011519657.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_011519659.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_016877491.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_016877493.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_054233465.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_054233466.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_054233467.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_054233468.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

XP_054233469.1

EC 2.3.1.24

EC 2.3.1.297

EC 2.3.1.298

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_042826.1 RefSeqGene

Range

20771..149326

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001290341.2 → NP_001277270.1 ceramide synthase 3 isoform 1

See identical proteins and their annotated locations for NP_001277270.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AC015723, AC027020, BC027616, BC034500, HY237628

UniProtKB/Swiss-Prot

Q8IU89

Conserved Domains (2) summary

cd00086
Location:93 → 139

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:142 → 335

TRAM_LAG1_CLN8; TLC domain
NM_001290342.2 → NP_001277271.1 ceramide synthase 3 isoform 2

See identical proteins and their annotated locations for NP_001277271.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC015723, AC027020, BC028703, BC034500, BC034970, HY022150, HY022670

Consensus CDS

CCDS10384.1

UniProtKB/Swiss-Prot

Q8IU89, Q8NE64, Q8NEN6

Related

ENSP00000437640.2, ENST00000538112.6

Conserved Domains (2) summary

cd00086
Location:82 → 128

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:131 → 324

TRAM_LAG1_CLN8; TLC domain
NM_001290343.2 → NP_001277272.1 ceramide synthase 3 isoform 2

See identical proteins and their annotated locations for NP_001277272.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC015723, AC027020, BC034500, BC034970

Consensus CDS

CCDS10384.1

UniProtKB/Swiss-Prot

Q8IU89, Q8NE64, Q8NEN6

Conserved Domains (2) summary

cd00086
Location:82 → 128

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:131 → 324

TRAM_LAG1_CLN8; TLC domain
NM_001378789.1 → NP_001365718.1 ceramide synthase 3 isoform 2

Status: REVIEWED

Source sequence(s)

AC015723, AC027020

Consensus CDS

CCDS10384.1

UniProtKB/Swiss-Prot

Q8IU89, Q8NE64, Q8NEN6

Related

ENSP00000506641.1, ENST00000679737.1

Conserved Domains (2) summary

cd00086
Location:82 → 128

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:131 → 324

TRAM_LAG1_CLN8; TLC domain
NM_178842.5 → NP_849164.2 ceramide synthase 3 isoform 2

See identical proteins and their annotated locations for NP_849164.2

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2, 3 and 4 encode the same isoform (2), which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC015723, AC027020, BC034500, BC034970

Consensus CDS

CCDS10384.1

UniProtKB/Swiss-Prot

Q8IU89, Q8NE64, Q8NEN6

Related

ENSP00000284382.4, ENST00000284382.8

Conserved Domains (2) summary

cd00086
Location:82 → 128

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:131 → 324

TRAM_LAG1_CLN8; TLC domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

100400395..100544683 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011521357.3 → XP_011519659.1 ceramide synthase 3 isoform X1

See identical proteins and their annotated locations for XP_011519659.1

Conserved Domains (2) summary

cd00086
Location:93 → 139

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:142 → 335

TRAM_LAG1_CLN8; TLC domain
XM_011521355.3 → XP_011519657.1 ceramide synthase 3 isoform X1

See identical proteins and their annotated locations for XP_011519657.1

Conserved Domains (2) summary

cd00086
Location:93 → 139

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:142 → 335

TRAM_LAG1_CLN8; TLC domain
XM_017022002.2 → XP_016877491.1 ceramide synthase 3 isoform X1

Conserved Domains (2) summary

cd00086
Location:93 → 139

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:142 → 335

TRAM_LAG1_CLN8; TLC domain
XM_017022004.2 → XP_016877493.1 ceramide synthase 3 isoform X2

UniProtKB/Swiss-Prot

Q8IU89, Q8NE64, Q8NEN6

Conserved Domains (2) summary

cd00086
Location:82 → 128

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03798
Location:131 → 324

TRAM_LAG1_CLN8; TLC domain