CERS4

ceramide synthase 4, the group of CERS class homeoboxes

Basic information

Region (hg38): 19:8206736-8262433

Previous symbols: [ "LASS4" ]

Links

ENSG00000090661 ∙ NCBI:79603 ∙ OMIM:615334 ∙ HGNC:23747 ∙ Uniprot:Q9HA82 ∙ 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 CERS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERS4 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				2	1	3
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	3	1

Variants in CERS4

This is a list of pathogenic ClinVar variants found in the CERS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8251159-G-A		not specified	Uncertain significance (May 28, 2024)
19-8251167-C-T		not specified	Uncertain significance (Apr 13, 2023)
19-8251168-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-8251173-T-A		not specified	Uncertain significance (Apr 26, 2023)
19-8251195-T-C		not specified	Uncertain significance (May 13, 2024)
19-8251208-C-T			Likely benign (Jan 01, 2023)
19-8251213-C-T		not specified	Uncertain significance (Nov 25, 2024)
19-8254500-T-A		not specified	Uncertain significance (Mar 18, 2024)
19-8254521-C-T		not specified	Uncertain significance (Aug 28, 2024)
19-8254569-G-A			Likely benign (May 18, 2018)
19-8254594-C-T		not specified	Uncertain significance (Dec 17, 2023)
19-8255644-C-T		not specified	Uncertain significance (Mar 28, 2022)
19-8255677-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-8255703-A-C		not specified	Uncertain significance (Nov 25, 2024)
19-8255842-T-C		not specified	Uncertain significance (Sep 08, 2024)
19-8255856-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-8256252-C-T		not specified	Uncertain significance (Nov 13, 2024)
19-8256613-T-A			Likely benign (Aug 01, 2024)
19-8256628-C-G		not specified	Uncertain significance (Apr 22, 2022)
19-8256648-C-G		not specified	Uncertain significance (Dec 26, 2023)
19-8256678-C-T			Benign (May 18, 2018)
19-8256691-C-G		not specified	Uncertain significance (Nov 08, 2022)
19-8256705-C-T		not specified	Uncertain significance (Sep 24, 2024)
19-8256959-A-T		not specified	Uncertain significance (Jul 08, 2021)
19-8256963-G-T		not specified	Uncertain significance (Jul 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERS4	protein_coding	protein_coding	ENST00000251363	10	55686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-22	0.0000892	125571	1	175	125747	0.000700

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.746	264	232	1.14	0.0000140	2537
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00118
Ashkenazi Jewish	0.00666	0.00657
East Asian	0.000275	0.000272
Finnish	0.000465	0.000462
European (Non-Finnish)	0.000385	0.000378
Middle Eastern	0.000275	0.000272
South Asian	0.000393	0.000392
Other	0.000660	0.000652

dbNSFP

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}.
• 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: 0.131

Intolerance Scores

• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.170
• ghis: 0.482

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cers4
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: sphingolipid biosynthetic process;ceramide biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;nuclear membrane
• Molecular function: DNA binding;sphingosine N-acyltransferase activity