CERS2

ceramide synthase 2, the group of CERS class homeoboxes

Basic information

Region (hg38): 1:150960582-150975003

Previous symbols: [ "LASS2" ]

Links

ENSG00000143418 ∙ NCBI:29956 ∙ OMIM:606920 ∙ HGNC:14076 ∙ Uniprot:Q96G23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CERS2 gene.

• Inborn genetic diseases (9 variants)
• not provided (4 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERS2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	3

Variants in CERS2

This is a list of pathogenic ClinVar variants found in the CERS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-150960754-C-G		not specified	Uncertain significance (Jan 09, 2024)
1-150960883-G-C		not specified	Uncertain significance (Dec 22, 2023)
1-150960918-T-C			Likely benign (Aug 01, 2018)
1-150960992-C-T			Likely benign (Feb 01, 2023)
1-150961124-C-T			Benign (Dec 31, 2019)
1-150962676-A-G		not specified	Uncertain significance (Jun 26, 2023)
1-150962697-C-T			Benign (Dec 31, 2019)
1-150963063-G-A			Likely benign (Feb 01, 2023)
1-150963129-G-T		not specified	Uncertain significance (Aug 13, 2021)
1-150963578-T-G		not specified	Uncertain significance (Jan 31, 2023)
1-150964005-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-150964262-G-T			Benign (Jun 21, 2018)
1-150964267-AACTT-A			Uncertain significance (Apr 24, 2023)
1-150966161-C-G		not specified	Uncertain significance (Sep 26, 2023)
1-150966174-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-150966204-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-150966264-G-C		not specified	Uncertain significance (Dec 08, 2023)
1-150966805-C-T			Likely benign (Jul 01, 2022)
1-150966842-G-A			Benign (Dec 31, 2019)
1-150966843-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-150967403-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-150967407-A-G			Benign (Dec 31, 2019)
1-150967418-T-G		not specified	Uncertain significance (Oct 29, 2021)
1-150967832-G-A			Benign (Dec 31, 2019)
1-150968135-G-A		Marfanoid habitus and intellectual disability	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERS2	protein_coding	protein_coding	ENST00000271688	10	14421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.480	0.520	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	158	234	0.676	0.0000144	2478
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000594	0.0000594
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Suppresses the growth of cancer cells. May be involved in sphingolipid synthesis.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.673
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cers2
• Phenotype: neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• 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
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;nuclear membrane
• Molecular function: DNA binding;protein binding;sphingosine N-acyltransferase activity