CERS5

ceramide synthase 5, the group of CERS class homeoboxes

Basic information

Region (hg38): 12:50129288-50167533

Previous symbols: [ "LASS5" ]

Links

ENSG00000139624 ∙ NCBI:91012 ∙ OMIM:615335 ∙ HGNC:23749 ∙ Uniprot:Q8N5B7 ∙ 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 CERS5 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERS5 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					1	1
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	1

Variants in CERS5

This is a list of pathogenic ClinVar variants found in the CERS5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50130562-A-G		not specified	Uncertain significance (May 06, 2022)
12-50130595-C-T		not specified	Uncertain significance (Apr 28, 2023)
12-50130693-A-G		not specified	Uncertain significance (Mar 12, 2024)
12-50134563-C-A		not specified	Uncertain significance (Nov 18, 2022)
12-50134691-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-50135790-G-A		not specified	Uncertain significance (May 30, 2022)
12-50135804-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-50135812-C-A		not specified	Uncertain significance (Nov 17, 2022)
12-50135993-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-50136009-T-G		not specified	Uncertain significance (Feb 05, 2024)
12-50137768-C-G		not specified	Uncertain significance (Jan 16, 2024)
12-50138603-C-G		not specified	Uncertain significance (Sep 25, 2023)
12-50142081-A-C		not specified	Uncertain significance (Nov 08, 2021)
12-50143099-T-C		not specified	Uncertain significance (Aug 28, 2023)
12-50143144-T-G		not specified	Uncertain significance (Jun 09, 2022)
12-50143179-C-A		not specified	Uncertain significance (Oct 30, 2023)
12-50143966-T-G		not specified	Uncertain significance (Jun 11, 2021)
12-50143973-C-A		not specified	Uncertain significance (Jul 14, 2021)
12-50144018-C-A		not specified	Uncertain significance (Aug 21, 2023)
12-50144020-C-T		not specified	Uncertain significance (Jul 14, 2023)
12-50144056-A-G		not specified	Uncertain significance (Jan 09, 2024)
12-50167136-C-T			Benign (Nov 20, 2018)
12-50167159-T-C		not specified	Uncertain significance (Mar 01, 2024)
12-50167197-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-50167204-G-C		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERS5	protein_coding	protein_coding	ENST00000317551	10	37714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.50e-9	0.875	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	165	214	0.771	0.0000109	2568
Missense in Polyphen		31	56.47	0.54896		711
Synonymous	1.86	57	77.9	0.732	0.00000379	733
Loss of Function	1.70	17	26.5	0.642	0.00000146	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dihydroceramide synthase. Catalyzes the acylation of sphingosine to form dihydroceramide, with high selectivity toward palmitoyl-CoA as acyl donor compared to stearoyl-CoA. Inhibited by fumonisin B1 (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: 0.111

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.385
• hipred: N
• hipred_score: 0.345
• ghis: 0.521

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: Cers5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; growth/size/body region 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