CERS4

protein-coding

ceramide synthase 4, the group of CERS class homeoboxes

Gene summary

Enables sphingosine N-acyltransferase activity. Involved in ceramide biosynthetic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LASS4

MANE transcript

NM_024552.3

Inheritance

—

ClinVar variants

U:94B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.24

Max pathogenic AF

—

Genomic locus

chr19:8,206,736-8,262,433

External References & Databases

Ensembl (ENSG00000090661)

Transcript & Mutation Effects

hg38 • Region Span ~55.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CERS4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024552.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			80 clinvar	2 clinvar		82
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	94	4	1	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 213 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024552.3	RefSeq	NP_078828.2	10	MANE Select
ENST00000251363.10	Ensembl	ENSP00000251363.5	10	MANE Select
ENST00000558268.5	Ensembl	ENSP00000453388.1	3	Standard
ENST00000558331.5	Ensembl	ENSP00000452753.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sphingolipid signaling pathway - Homo sapiens (human)
Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Metabolism of lipids
Metabolism

Biological Process

sphingolipid biosynthetic process
ceramide biosynthetic process

Molecular Function

DNA binding
sphingosine N-acyltransferase activity

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251363
Coding exons: 10
Length: 55686
Individuals with no LoFs: 125571
Homozygous LoFs: 1
Heterozygous LoFs: 175
Defined: 125747
p: 0.000700

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.746	264	232	1.14	0.0000140	2537
Missense (PolyPhen)		91	79.534	1.1442		870
Synonymous	-0.0159	101	101	1.00	0.00000643	787
Loss of Function	-1.11	30	24.1	1.24	0.00000137	225

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00094	0.00093	rare
Ashkenazi Jewish	0.0067	0.0066	notable
East Asian	0.00027	0.00027	rare
Finnish	0.00046	0.00046	rare
European (Non-Finnish)	0.00038	0.00038	rare
South Asian	0.00039	0.00039	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be either a bona fide (dihydro)ceramide synthase or a modulator of its activity. When overexpressed in cells is involved in the production of sphingolipids containing different fatty acid donors (N-linked stearoyl- (C18) or arachidoyl- (C20) ceramides) in a fumonisin B1-independent manner (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.131

Intolerance Scores

RVIS EVS: 0.09
RVIS percentile EVS: 60.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium