CERS3 (ceramide synthase 3)

Gene

• Entrez ID: 204219
• Gene name: Ceramide synthase 3
• Gene symbol: CERS3
• Synonyms (NCBI Gene): ARCI9, LASS3
• Chromosome: 15
• Chromosome location: 15q26.3
• 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 synth

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587776996	C>A	Pathogenic	Splice donor variant
rs762679102	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs1567644030	C>T	Pathogenic	Coding sequence variant, stop gained
rs1596772428	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT886964	hsa-miR-1207-5p	CLIP-seq
MIRT886965	hsa-miR-1227	CLIP-seq
MIRT886966	hsa-miR-1288	CLIP-seq
MIRT886967	hsa-miR-29a	CLIP-seq
MIRT886968	hsa-miR-29b	CLIP-seq
MIRT886969	hsa-miR-29c	CLIP-seq
MIRT886970	hsa-miR-3199	CLIP-seq
MIRT886971	hsa-miR-4311	CLIP-seq
MIRT886972	hsa-miR-4330	CLIP-seq
MIRT886973	hsa-miR-4514	CLIP-seq
MIRT886974	hsa-miR-4692	CLIP-seq
MIRT886975	hsa-miR-4712-3p	CLIP-seq
MIRT886976	hsa-miR-4715-3p	CLIP-seq
MIRT886977	hsa-miR-4736	CLIP-seq
MIRT886978	hsa-miR-4755-3p	CLIP-seq
MIRT886979	hsa-miR-4763-3p	CLIP-seq
MIRT886980	hsa-miR-548aa	CLIP-seq
MIRT886981	hsa-miR-548ac	CLIP-seq
MIRT886982	hsa-miR-548d-3p	CLIP-seq
MIRT886983	hsa-miR-548z	CLIP-seq
MIRT886984	hsa-miR-940	CLIP-seq
MIRT886964	hsa-miR-1207-5p	CLIP-seq
MIRT1963022	hsa-miR-1264	CLIP-seq
MIRT1963023	hsa-miR-150	CLIP-seq
MIRT1963024	hsa-miR-1827	CLIP-seq
MIRT1963025	hsa-miR-19a	CLIP-seq
MIRT1963026	hsa-miR-19b	CLIP-seq
MIRT1963027	hsa-miR-3612	CLIP-seq
MIRT1963028	hsa-miR-3667-3p	CLIP-seq
MIRT1963029	hsa-miR-4300	CLIP-seq
MIRT886979	hsa-miR-4763-3p	CLIP-seq
MIRT1963030	hsa-miR-650	CLIP-seq
MIRT1963031	hsa-miR-920	CLIP-seq
MIRT886984	hsa-miR-940	CLIP-seq
MIRT2199439	hsa-miR-10a	CLIP-seq
MIRT2199440	hsa-miR-10b	CLIP-seq
MIRT2199441	hsa-miR-1200	CLIP-seq
MIRT886964	hsa-miR-1207-5p	CLIP-seq
MIRT886965	hsa-miR-1227	CLIP-seq
MIRT2199442	hsa-miR-1253	CLIP-seq
MIRT2199443	hsa-miR-1266	CLIP-seq
MIRT2199444	hsa-miR-15a	CLIP-seq
MIRT2199445	hsa-miR-15b	CLIP-seq
MIRT2199446	hsa-miR-16	CLIP-seq
MIRT2199447	hsa-miR-195	CLIP-seq
MIRT1963025	hsa-miR-19a	CLIP-seq
MIRT1963026	hsa-miR-19b	CLIP-seq
MIRT2199448	hsa-miR-24	CLIP-seq
MIRT2199449	hsa-miR-3119	CLIP-seq
MIRT2199450	hsa-miR-3126-5p	CLIP-seq
MIRT2199451	hsa-miR-3127-5p	CLIP-seq
MIRT2199452	hsa-miR-3151	CLIP-seq
MIRT2199453	hsa-miR-342-5p	CLIP-seq
MIRT2199454	hsa-miR-3912	CLIP-seq
MIRT2199455	hsa-miR-3918	CLIP-seq
MIRT2199456	hsa-miR-3944-5p	CLIP-seq
MIRT2199457	hsa-miR-424	CLIP-seq
MIRT2199458	hsa-miR-4324	CLIP-seq
MIRT2199459	hsa-miR-4419a	CLIP-seq
MIRT2199460	hsa-miR-4434	CLIP-seq
MIRT2199461	hsa-miR-4436b-3p	CLIP-seq
MIRT2199462	hsa-miR-4437	CLIP-seq
MIRT2199463	hsa-miR-4447	CLIP-seq
MIRT2199464	hsa-miR-4472	CLIP-seq
MIRT2199465	hsa-miR-4510	CLIP-seq
MIRT2199466	hsa-miR-4516	CLIP-seq
MIRT2199467	hsa-miR-4518	CLIP-seq
MIRT2199468	hsa-miR-4651	CLIP-seq
MIRT2199469	hsa-miR-4664-5p	CLIP-seq
MIRT886975	hsa-miR-4712-3p	CLIP-seq
MIRT886977	hsa-miR-4736	CLIP-seq
MIRT886978	hsa-miR-4755-3p	CLIP-seq
MIRT886979	hsa-miR-4763-3p	CLIP-seq
MIRT2199470	hsa-miR-4768-3p	CLIP-seq
MIRT2199471	hsa-miR-491-5p	CLIP-seq
MIRT2199472	hsa-miR-497	CLIP-seq
MIRT2199473	hsa-miR-544b	CLIP-seq
MIRT2199474	hsa-miR-608	CLIP-seq
MIRT2199475	hsa-miR-622	CLIP-seq
MIRT2199476	hsa-miR-665	CLIP-seq
MIRT886984	hsa-miR-940	CLIP-seq
MIRT2427317	hsa-miR-375	CLIP-seq
MIRT2427318	hsa-miR-4727-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	ISS
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	IEA
GO:0008544	Process	Epidermis development	IEA
GO:0008544	Process	Epidermis development	ISS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030148	Process	Sphingolipid biosynthetic process	IEA
GO:0030148	Process	Sphingolipid biosynthetic process	TAS
GO:0030216	Process	Keratinocyte differentiation	IMP	23754960
GO:0046513	Process	Ceramide biosynthetic process	IBA
GO:0046513	Process	Ceramide biosynthetic process	IDA	17977534, 22038835
GO:0046513	Process	Ceramide biosynthetic process	IEA
GO:0046513	Process	Ceramide biosynthetic process	IMP	23754960
GO:0050291	Function	Sphingosine N-acyltransferase activity	IBA
GO:0050291	Function	Sphingosine N-acyltransferase activity	IDA	17977534, 22038835
GO:0050291	Function	Sphingosine N-acyltransferase activity	IEA
GO:0050291	Function	Sphingosine N-acyltransferase activity	TAS
GO:0070268	Process	Cornification	IEA
GO:0070268	Process	Cornification	ISS

Other IDs

• MIM: 615276
• HGNC: 23752
• e!Ensembl: ENSG00000154227

Protein

• UniProt ID: Q8IU89
• Protein name: Ceramide synthase 3 (CerS3) (Dihydroceramide synthase 3) (LAG1 longevity assurance homolog 3) (Sphingosine N-acyltransferase CERS3) (EC 2.3.1.24) (Ultra-long-chain ceramide synthase CERS3) (EC 2.3.1.298) (Very-long-chain ceramide synthase CERS3) (EC 2.3.1
• Protein function: Ceramide synthase that catalyzes the transfer of the acyl chain from acyl-CoA to a sphingoid base, with high selectivity toward very- and ultra-long-chain fatty acyl-CoA (chain length greater than C22) (PubMed:17977534, PubMed:22038835, PubMed:2
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	71 → 126	Homeodomain	Domain
  PF03798	TRAM_LAG1_CLN8	131 → 324	TLC domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the epidermis, where it localizes at the interface between the stratum granulosum and the stratum corneum (at protein level). {ECO:0000269|PubMed:23754960}.
• Sequence:

  MFWTFKEWFWLERFWLPPTIKWSDLEDHDGLVFVKPSHLYVTIPYAFLLLIIRRVFEKFV
  ASPLAKSFGIKETVRKVTPNTVLENFFKHSTRQPLQTDIYGLAKKCNLTERQVERWFRSR
  RNQERPSRLKKFQEACWRFAFYLMITVAGIAFLYDKPWLYDLWEVWNGYPKQPLLPSQYW
  YYILEMSFYWSLLFRLGFDVKRKDFLAHIIHHLAAISLMSFSWCANYIRSGTLVMIVHDV
  ADIWLESAKMFSYAGWTQTCNTLFFIFSTIFFISRLIVFPFWILYCTLILPMYHLEPFFS
  YIFLNLQLMILQVLHLYWGYYILKMLNRCIFMKSIQDVRSDDEDYEEEEEEEEEEATKGK
  EMDCLKNGLRAERHLIPNGQHGH

• Sequence length: 383

Pathways

KEGG:

Sphingolipid metabolism
Metabolic pathways
Sphingolipid signaling pathway

Reactome:

Sphingolipid de novo biosynthesis

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormality of the skin	Likely pathogenic	rs1256164950, rs747911784	RCV001814463 RCV001814456	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal recessive congenital ichthyosis 9	Likely pathogenic; Pathogenic	rs747911784, rs2549119804, rs1567644030, rs587776996, rs762679102, rs1596772428	RCV005005254 RCV003490905 RCV000782388 RCV000049259 RCV000054808 RCV000991456	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Ichthyosis	Likely pathogenic	rs587776996	RCV004798762	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Lamellar ichthyosis	Pathogenic	rs752230253	RCV003123559	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BEHCET'S SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CERS3-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL ICHTHYOSIFORM ERYTHRODERMA	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NON-BULLOUS ICHTHYOSIFORM ERYTHRODERMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NONBULLOUS ICHTHYOSIFORM ERYTHRODERMA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ICHTHYOSES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alopecia	Alopecia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Blood Coagulation Disorders Inherited	Blood coagulation disorder	Pubtator	39501396	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	21998744	Associate	★☆☆☆☆ Found in Text Mining only
Congenital ichthyosis	Congenital Ichthyosis	BEFREE	23549421, 23754960, 28875980		★☆☆☆☆ Found in Text Mining only
Congenital non-bullous ichthyosiform erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Nonbullous Ichthyosiform Erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma	BEFREE	23549421, 23754960, 28875980		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Nonbullous Ichthyosiform Erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma	ORPHANET_DG	23549421		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corneal erosion	Corneal erosion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dermatitis	Dermatitis	BEFREE	30838224		★☆☆☆☆ Found in Text Mining only
Dermatitis, Atopic	Dermatitis	BEFREE	30838224		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ectropion	Ectropion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Eczema	Eczema	BEFREE	30838224		★☆☆☆☆ Found in Text Mining only
Exfoliative dermatitis	Exfoliative Dermatitis	BEFREE	23549421		★☆☆☆☆ Found in Text Mining only
Exfoliative dermatitis	Exfoliative Dermatitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypohidrosis	Hypohidrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ichthyoses	Ichthyosis	BEFREE	28875980		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ichthyoses	Ichthyosis	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ichthyosiform Erythroderma, Congenital	Ichthyosis Congenita	BEFREE	23549421, 23754960, 28875980		★☆☆☆☆ Found in Text Mining only
Ichthyosiform Erythroderma, Congenital	Ichthyosis Congenita	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ichthyosis	Ichthyosis	Pubtator	28875980, 33492757, 34983512	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 9	Ichthyosis with hypotrichosis	GENOMICS_ENGLAND_DG	23549421, 23754960		★☆☆☆☆ Found in Text Mining only
ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 9	Ichthyosis with hypotrichosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 9	Ichthyosis with hypotrichosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Ichthyosis-short stature-brachydactyly-microspherophakia syndrome	Ichthyosis-Short Stature-Brachydactyly-Microspherophakia Syndrome	Orphanet			★☆☆☆☆ Found in Text Mining only
Keratitis	Keratitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratoderma, Palmoplantar	Palmoplantar keratoderma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lamellar ichthyosis type 3	Lamellar ichthyosis	Pubtator	28875980, 33492757	Associate	★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome	Metabolic syndrome	Pubtator	36011408	Associate	★☆☆☆☆ Found in Text Mining only
Weill-Marchesani-Like Syndrome	Weill-Marchesani Syndrome	ORPHANET_DG	23754960		★☆☆☆☆ Found in Text Mining only