AtlasGene
ACER3
alkaline ceramidase 3
- HGNC 16066↗(opens in a new tab)
- Ensembl gene ENSG00000078124↗(opens in a new tab)
- NCBI Gene 55331↗(opens in a new tab)
Summary
- Cytogenetic location
- 11q13.5
- Coordinates
- Chromosome 11: 76,860,918–77,026,797 (GRCh38)
- Exons
- 11 exons across 165.9 kb
- Protein
- 267 amino acids
- Also known as
- FLJ11238, APHC
- Previous symbols
- PHCA
- MANE Select transcript
- ENST00000532485.6NM_018367.7
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Get my Genome TestCurated report relevant to this gene
Other Inherited Leukodystrophies
- Leukodystrophy (other and unspecified types)
One of 80 genes linked to it
Inherited conditions that damage or prevent the normal formation of myelin, the white matter of the brain and spinal cord. Different types follow autosomal recessive, autosomal dominant or X-linked inheritance depending on the gene involved.
- 1 GenCC submitter rates it definitive or strong
▶Actionability
Knowing the specific genetic cause can end a diagnostic search, guide supportive care and surveillance, show whether a specific treatment exists, and allow testing of relatives.
How ACER3 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 7.3 kb of the gene's 165.9 kb; 804 of those bases code for the protein.
Sequencing ACER3
2Easy
How hard ACER3 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of ACER3's exons sit where short reads map cleanly.
What adds to it: the share of ACER3's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.2.6%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.7.7%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.4.2%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of ACER3's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
5
positions in ACER3 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 165.9 kb of ACER3, introns included, not only the 7.3 kb of exons.
ClinVar pathogenic variants (5)
The ACER3 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 3
- Likely pathogenic 2
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_018367.7(ACER3):c.607C>T (p.Arg203Ter) (opens in a new tab) | alkaline ceramidase 3 deficiency | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018367.7(ACER3):c.631G>T (p.Gly211Cys) (opens in a new tab) | alkaline ceramidase 3 deficiency | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018367.7(ACER3):c.703A>C (p.Ser235Arg) (opens in a new tab) | alkaline ceramidase 3 deficiency | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018367.7(ACER3):c.475C>T (p.Arg159Ter) (opens in a new tab) | alkaline ceramidase 3 deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_018367.7(ACER3):c.587G>A (p.Cys196Tyr) (opens in a new tab) | alkaline ceramidase 3 deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
- AARS1alanyl-tRNA synthetase 1Shares 1 condition
- AARS2alanyl-tRNA synthetase 2, mitochondrialShares 1 condition
- ABCD1ATP binding cassette subfamily D member 1Shares 1 condition
- ADARadenosine deaminase RNA specificShares 1 condition
- AIMP1aminoacyl tRNA synthetase complex interacting multifunctional protein 1Shares 1 condition
- AIMP2aminoacyl tRNA synthetase complex interacting multifunctional protein 2Shares 1 condition
- ALDH3A2aldehyde dehydrogenase 3 family member A2Shares 1 condition
- ARSAarylsulfatase AShares 1 condition
- ASPAaspartoacylaseShares 1 condition
- ATP11AATPase phospholipid transporting 11AShares 1 condition
- CLCN2chloride voltage-gated channel 2Shares 1 condition
- CLDN11claudin 11Shares 1 condition
Traits linked to ACER3
The Human Phenotype Ontology lists these as features of the rare conditions ACER3 can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-18: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-8b139e39.
Cite this page
Dante Labs. (n.d.). ACER3 gene: alkaline ceramidase 3. Retrieved 18 October 2026, from https://dantelabs.com/genes/acer3
Dante Labs. ACER3 gene: alkaline ceramidase 3 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/acer3
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