ACER1

alkaline ceramidase 1, the group of Alkaline ceramidases

Basic information

Region (hg38): 19:6306142-6333612

Previous symbols: [ "ASAH3" ]

Links

ENSG00000167769 ∙ NCBI:125981 ∙ OMIM:613491 ∙ HGNC:18356 ∙ Uniprot:Q8TDN7 ∙ 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 ACER1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACER1 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						0
missense			18	2	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	1

Variants in ACER1

This is a list of pathogenic ClinVar variants found in the ACER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6306737-G-A		not specified	Uncertain significance (Nov 02, 2023)
19-6306751-G-A		not specified	Uncertain significance (Jan 24, 2025)
19-6306775-C-T		not specified	Uncertain significance (Aug 30, 2022)
19-6306794-T-C		not specified	Uncertain significance (Nov 18, 2022)
19-6306836-C-T		not specified	Uncertain significance (Feb 01, 2025)
19-6306846-C-T			Likely benign (May 04, 2018)
19-6306848-T-C		not specified	Uncertain significance (Sep 21, 2023)
19-6307168-T-C		not specified	Uncertain significance (Jul 31, 2024)
19-6307207-C-G		not specified	Uncertain significance (Nov 17, 2023)
19-6307208-G-A		not specified	Uncertain significance (Sep 13, 2023)
19-6307235-C-T			Benign (May 04, 2018)
19-6309751-G-C		not specified	Uncertain significance (Jul 25, 2023)
19-6309758-C-T		not specified	Uncertain significance (Feb 21, 2024)
19-6309773-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-6309820-C-T		not specified	Uncertain significance (Mar 14, 2023)
19-6309834-C-A		not specified	Uncertain significance (Mar 23, 2022)
19-6312158-C-G		not specified	Uncertain significance (May 24, 2023)
19-6312248-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-6312263-G-A		not specified	Uncertain significance (Jun 29, 2023)
19-6312412-C-T		not specified	Likely benign (Oct 01, 2024)
19-6312424-G-A		not specified	Uncertain significance (Dec 25, 2024)
19-6312430-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-6312478-T-C		not specified	Uncertain significance (Apr 05, 2023)
19-6312483-A-G		not specified	Uncertain significance (Apr 04, 2023)
19-6333473-C-T		not specified	Uncertain significance (Feb 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACER1	protein_coding	protein_coding	ENST00000301452	6	27488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00217	0.925	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	147	163	0.901	0.00000968	1746
Missense in Polyphen		56	55.54	1.0083		658
Synonymous	-0.555	69	63.4	1.09	0.00000391	491
Loss of Function	1.57	6	11.8	0.508	5.05e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000169	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000177	0.000163
Other	0.000509	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes the sphingolipid ceramide into sphingosine and free fatty acid at an optimal pH of 8.0. Has a highly restricted substrate specificity for the natural stereoisomer of ceramide with D-erythro-sphingosine but not D-ribo- phytosphingosine or D-erythro-dihydrosphingosine as a backbone. May have a role in regulating the levels of bioactive lipids ceramide and sphingosine 1-phosphate, as well as complex sphingolipids (By similarity). {ECO:0000250}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Sphingolipid Metabolism;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.504
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.0928
• hipred: N
• hipred_score: 0.352
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acer1
• Phenotype: hematopoietic system phenotype; pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye 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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: sphingolipid metabolic process;epidermis development;response to alkaline pH;regulation of lipid metabolic process;sphingolipid biosynthetic process;cell differentiation;keratinocyte differentiation;sphingosine biosynthetic process;ceramide catabolic process;cellular response to calcium ion
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: N-acylsphingosine amidohydrolase activity;dihydroceramidase activity;ceramidase activity