ASAH2

N-acylsphingosine amidohydrolase 2

Basic information

Region (hg38): 10:50182778-50279720

Links

ENSG00000188611 ∙ NCBI:56624 ∙ OMIM:611202 ∙ HGNC:18860 ∙ Uniprot:Q9NR71 ∙ 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 ASAH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASAH2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in ASAH2

This is a list of pathogenic ClinVar variants found in the ASAH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-50214744-C-G		not specified	Uncertain significance (Dec 14, 2021)
10-50214780-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-50218534-C-A		not specified	Uncertain significance (Jul 11, 2023)
10-50234545-T-G		not specified	Uncertain significance (Oct 05, 2021)
10-50243242-C-T		not specified	Uncertain significance (Feb 01, 2023)
10-50243257-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-50243351-T-C		not specified	Uncertain significance (Feb 28, 2024)
10-50245244-C-A		not specified	Uncertain significance (Nov 07, 2023)
10-50245346-G-A		not specified	Uncertain significance (Oct 29, 2021)
10-50245361-G-A		not specified	Uncertain significance (Oct 29, 2021)
10-50245386-G-A		not specified	Uncertain significance (Jul 27, 2022)
10-50248499-T-C		not specified	Uncertain significance (Jun 03, 2022)
10-50248512-G-C		not specified	Uncertain significance (Dec 15, 2022)
10-50248514-T-C		not specified	Uncertain significance (Aug 15, 2023)
10-50248547-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASAH2	protein_coding	protein_coding	ENST00000395526	20	65833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00427	0.877	124583	9	1156	125748	0.00464

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	123	134	0.916	0.00000686	5076
Missense in Polyphen		38	39.644	0.95852		1949
Synonymous	-1.46	62	49.0	1.27	0.00000246	1516
Loss of Function	1.32	5	9.36	0.534	5.62e-7	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0131	0.0130
Ashkenazi Jewish	0.00397	0.00398
East Asian	0.000218	0.000217
Finnish	0.00864	0.00863
European (Non-Finnish)	0.00581	0.00578
Middle Eastern	0.000218	0.000217
South Asian	0.000849	0.000850
Other	0.00391	0.00375

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes the sphingolipid ceramide into sphingosine and free fatty acid at an optimal pH of 6.5-8.5 (PubMed:10781606, PubMed:26190575). Acts as a key regulator of sphingolipid signaling metabolites by generating sphingosine at the cell surface. Acts as a repressor of apoptosis both by reducing C16- ceramide, thereby preventing ceramide-induced apoptosis, and generating sphingosine, a precursor of the antiapoptotic factor sphingosine 1-phosphate. Probably involved in the digestion of dietary sphingolipids in intestine by acting as a key enzyme for the catabolism of dietary sphingolipids and regulating the levels of bioactive sphingolipid metabolites in the intestinal tract. {ECO:0000269|PubMed:10781606, ECO:0000269|PubMed:15946935, ECO:0000269|PubMed:16061940, ECO:0000269|PubMed:26190575}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.129

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asah2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: sphingosine metabolic process;ceramide metabolic process;apoptotic process;response to organic substance;long-chain fatty acid biosynthetic process;sphingosine biosynthetic process;ceramide catabolic process
• Cellular component: extracellular region;mitochondrion;plasma membrane;integral component of membrane
• Molecular function: calcium ion binding;zinc ion binding;N-acylsphingosine amidohydrolase activity;ceramidase activity