ACER2
alkaline ceramidase 2, the group of Alkaline ceramidases
Basic information
Region (hg38): 9:19409009-19452505
Previous symbols: [ "ASAH3L" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACER2 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 | 22 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 22 | 2 | 0 |
Variants in ACER2
This is a list of pathogenic ClinVar variants found in the ACER2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-19409102-G-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 9-19409117-G-T | not specified | Uncertain significance (Aug 02, 2022) | ||
| 9-19409153-C-G | not specified | Uncertain significance (Aug 11, 2022) | ||
| 9-19409172-A-G | not specified | Uncertain significance (Oct 12, 2021) | ||
| 9-19409181-T-C | not specified | Uncertain significance (Jun 10, 2024) | ||
| 9-19409185-A-G | not specified | Uncertain significance (Aug 10, 2021) | ||
| 9-19423877-T-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 9-19423889-C-T | not specified | Uncertain significance (Feb 11, 2022) | ||
| 9-19423905-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 9-19423974-T-G | not specified | Uncertain significance (Mar 24, 2023) | ||
| 9-19424812-G-T | not specified | Uncertain significance (Dec 06, 2023) | ||
| 9-19424840-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 9-19434951-A-G | not specified | Uncertain significance (Aug 02, 2021) | ||
| 9-19434957-A-C | not specified | Uncertain significance (Jan 20, 2023) | ||
| 9-19434972-G-A | not specified | Uncertain significance (Jul 12, 2023) | ||
| 9-19435021-A-G | not specified | Uncertain significance (May 30, 2024) | ||
| 9-19446291-A-G | not specified | Likely benign (Mar 20, 2023) | ||
| 9-19446305-G-T | not specified | Uncertain significance (May 31, 2023) | ||
| 9-19446312-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 9-19446319-C-T | not specified | Uncertain significance (Jul 29, 2023) | ||
| 9-19446364-G-A | not specified | Uncertain significance (Sep 12, 2023) | ||
| 9-19446400-C-T | not specified | Uncertain significance (Mar 28, 2023) | ||
| 9-19450476-A-G | not specified | Uncertain significance (Jun 02, 2023) | ||
| 9-19450539-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 9-19450557-A-G | not specified | Likely benign (Jun 07, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ACER2 | protein_coding | protein_coding | ENST00000340967 | 6 | 43094 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0402 | 0.954 | 125723 | 0 | 25 | 125748 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.374 | 166 | 153 | 1.08 | 0.00000800 | 1783 |
| Missense in Polyphen | 65 | 62.522 | 1.0396 | 699 | ||
| Synonymous | -0.566 | 67 | 61.4 | 1.09 | 0.00000344 | 524 |
| Loss of Function | 2.41 | 5 | 15.1 | 0.330 | 7.33e-7 | 155 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000483 | 0.000468 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes the sphingolipid ceramide into sphingosine and free fatty acid. Unsaturated long-chain ceramides are the best substrates, saturated long-chain ceramides and unsaturated very long-chain ceramides are good substrates, whereas saturated very long-chain ceramides and short-chain ceramides were poor substrates. The substrate preference is D-erythro-C(18:1)-, C(20:1)-, C(20:4)-ceramide > D-erythro-C(16:0)-, C(18:0), C(20:0)- ceramide > D-erythro-C(24:1)-ceramide > D-erythro-C(12:0)- ceramide, D-erythro-C(14:0)-ceramides > D-erythro-C(24:0)-ceramide > D-erythro-C(6:0)-ceramide. Inhibits the maturation of protein glycosylation in the Golgi complex, including that of integrin beta-1 (ITGB1) and of LAMP1, by increasing the levels of sphingosine. Inhibits cell adhesion by reducing the level of ITGB1 in the cell surface. May have a role in cell proliferation and apoptosis that seems to depend on the balance between sphingosine and sphingosine-1-phosphate. {ECO:0000269|PubMed:16940153, ECO:0000269|PubMed:18945876, ECO:0000269|PubMed:20089856}.;
- Pathway
- Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.0858
Intolerance Scores
- loftool
- 0.724
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.76
Haploinsufficiency Scores
- pHI
- 0.208
- hipred
- N
- hipred_score
- 0.267
- ghis
- 0.422
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.900
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Acer2
- Phenotype
- homeostasis/metabolism phenotype; normal 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);
Gene ontology
- Biological process
- negative regulation of cell-matrix adhesion;ceramide metabolic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of cell population proliferation;positive regulation of cell death;sphingolipid biosynthetic process;response to retinoic acid;negative regulation of cell adhesion mediated by integrin;cellular response to drug;sphingosine biosynthetic process;negative regulation of protein glycosylation in Golgi
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of Golgi membrane
- Molecular function
- N-acylsphingosine amidohydrolase activity;dihydroceramidase activity;ceramidase activity