CERS6

protein-coding

ceramide synthase 6, the group of CERS class homeoboxes|MicroRNA protein coding host genes

Gene summary

Enables sphingosine N-acyltransferase activity. Involved in ceramide biosynthetic process. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

LASS6

MANE transcript

NM_203463.3

Inheritance

—

ClinVar variants

U:45B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr2:168,456,249-168,775,134

External References & Databases

Ensembl (ENSG00000172292)

Transcript & Mutation Effects

hg38 • Region Span ~318.9 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 CERS6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203463.3. 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	1 clinvar	3
missense			42 clinvar	3 clinvar	1 clinvar	46
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	45	5	2	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203463.3	RefSeq	NP_982288.1	10	MANE Select
ENST00000305747.11	Ensembl	ENSP00000306579.6	10	MANE Select
NM_001256126.2	RefSeq	NP_001243055.1	11	Standard
ENST00000392687.4	Ensembl	ENSP00000376453.4	11	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

regulation of transcription by RNA polymerase II
sphingolipid biosynthetic process
ceramide biosynthetic process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
sphingosine N-acyltransferase activity

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
membrane
integral component of membrane
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392687
Coding exons: 11
Length: 319273
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.657	191	218	0.875	0.0000112	2577
Missense (PolyPhen)		77	107.93	0.71341		1299
Synonymous	-0.443	90	84.8	1.06	0.00000486	728
Loss of Function	3.53	8	28.2	0.283	0.00000159	284

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in sphingolipid synthesis or its regulation. {ECO:0000250}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

RVIS EVS: 0.22
RVIS percentile EVS: 68.27

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	Medium
Cancer	Medium	Medium	Medium