CERS6

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

Basic information

Region (hg38): 2:168456248-168775134

Previous symbols: [ "LASS6" ]

Links

ENSG00000172292 ∙ NCBI:253782 ∙ OMIM:615336 ∙ HGNC:23826 ∙ Uniprot:Q6ZMG9 ∙ 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 CERS6 gene.

• Inborn genetic diseases (9 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERS6 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	2
missense			7	1	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	7	2	2

Variants in CERS6

This is a list of pathogenic ClinVar variants found in the CERS6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-168456478-C-A		not specified	Uncertain significance (Dec 05, 2022)
2-168456501-A-G		not specified	Uncertain significance (Aug 28, 2021)
2-168547596-A-G		not specified	Likely benign (Aug 08, 2023)
2-168547606-A-G		not specified	Uncertain significance (Dec 19, 2023)
2-168547610-C-G		not specified	Uncertain significance (Dec 19, 2023)
2-168547658-C-T		not specified	Uncertain significance (Dec 05, 2022)
2-168631004-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-168691053-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-168695040-A-G		not specified	Uncertain significance (Jun 05, 2023)
2-168715008-G-T		not specified	Uncertain significance (Dec 13, 2023)
2-168715009-C-T			Benign (Jun 04, 2018)
2-168715028-C-G		not specified	Uncertain significance (Jul 13, 2022)
2-168715100-C-G			Benign (May 24, 2018)
2-168717938-G-A		not specified	Likely benign (Oct 06, 2021)
2-168765629-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-168765662-C-T			Likely benign (Jun 04, 2018)
2-168765723-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-168769600-A-C		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERS6	protein_coding	protein_coding	ENST00000392687	11	319273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0386	0.961	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.657	191	218	0.875	0.0000112	2577
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000628	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in sphingolipid synthesis or its regulation. {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: 0.120

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.545
• hipred: Y
• hipred_score: 0.595
• ghis: 0.523

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: Cers6
• Phenotype: 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); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;sphingolipid biosynthetic process;ceramide biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;nuclear membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;sphingosine N-acyltransferase activity