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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 3 of 3.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_133492.3	NP_597999.1	6	yes	-
ENST00000301452.5	ENSP00000301452.3	6	yes	-
XM_011527673.3	XP_011525975.1	5	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACER1 gene.

• not_specified (49 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_133492.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			44	5	1	50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	45	6	1

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
		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

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

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