CERS2

protein-coding

ceramide synthase 2, the group of CERS class homeoboxes

Gene summary

This gene encodes a protein that has sequence similarity to yeast longevity assurance gene 1. Mutation or overexpression of the related gene in yeast has been shown to alter yeast lifespan. The human protein may play a role in the regulation of cell growth. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

Previous symbols:

LASS2

MANE transcript

NM_022075.5

Inheritance

—

ClinVar variants

U:54B:7

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr1:150,960,583-150,975,003

External References & Databases

Ensembl (ENSG00000143418)

Transcript & Mutation Effects

hg38 • Region Span ~14.4 kb

Loading mutation effect viewer...

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 CERS2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 4

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022075.5. 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			1 clinvar		3 clinvar	4
missense			46 clinvar	4 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	54	4	3	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 73 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022075.5	RefSeq	NP_071358.1	10	MANE Select
ENST00000368954.10	Ensembl	ENSP00000357950.5	10	MANE Select
NM_181746.4	RefSeq	NP_859530.1	10	Standard
ENST00000271688.10	Ensembl	ENSP00000271688.6	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
negative regulation of axon regeneration
negative regulation of Schwann cell migration
negative regulation of Schwann cell proliferation involved in axon regeneration

Molecular Function

DNA binding
protein 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: ENST00000271688
Coding exons: 10
Length: 14421
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	158	234	0.676	0.0000144	2478
Missense (PolyPhen)		34	92.854	0.36617		961
Synonymous	-0.452	89	83.7	1.06	0.00000463	733
Loss of Function	3.83	6	27.8	0.216	0.00000168	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Suppresses the growth of cancer cells. May be involved in sphingolipid synthesis.;

Recessive Scores

pRec: 0.145

Intolerance Scores

RVIS EVS: -0.14
RVIS percentile EVS: 43.57

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