AtlasGene
AP1S1
adaptor related protein complex 1 subunit sigma 1
- HGNC 559↗(opens in a new tab)
- Ensembl gene ENSG00000106367↗(opens in a new tab)
- NCBI Gene 1174↗(opens in a new tab)
Summary
- Cytogenetic location
- 7q22.1
- Coordinates
- Chromosome 7: 101,154,476–101,161,276 (GRCh38)
- Exons
- 5 exons across 6.8 kb
- Protein
- 158 amino acids
- Also known as
- AP19, SIGMA1A, WUGSC:H_DJ0747G18.2
- Previous symbols
- CLAPS1, EKV3
- MANE Select transcript
- ENST00000337619.11NM_001283.5
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Disorder of Copper Metabolism
An inherited metabolic disease that is has its basis in the disruption of cellular copper ion homeostasis.
- ClinGen rates the link definitive
- 4 GenCC submitters rate it definitive or strong
How AP1S1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
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 1.2 kb of the gene's 6.8 kb; 477 of those bases code for the protein.
Sequencing AP1S1
4Easy
How hard AP1S1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of AP1S1's exons sit where short reads map cleanly.
What adds to it: the share of AP1S1'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%.0%
- 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%.7.1%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.25%
- 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 AP1S1'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.
6
positions in AP1S1 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 6.8 kb of AP1S1, introns included, not only the 1.2 kb of exons.
ClinVar pathogenic variants (7)
The AP1S1 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 1
- Pathogenic/likely pathogenic 1
- Likely pathogenic 5
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_001283.5(AP1S1):c.186T>G (p.Tyr62Ter) (opens in a new tab) | MEDNIK syndrome | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_001283.5(AP1S1):c.183-2A>G (opens in a new tab) | MEDNIK syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001283.5(AP1S1):c.183-1G>C (opens in a new tab) | MEDNIK syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001283.5(AP1S1):c.220C>T (p.Gln74Ter) (opens in a new tab) | MEDNIK syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001283.5(AP1S1):c.291+2T>A (opens in a new tab) | MEDNIK syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001283.5(AP1S1):c.364dup (p.Asp122fs) (opens in a new tab) | MEDNIK syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001283.5(AP1S1):c.364del (p.Asp122fs) (opens in a new tab) | MEDNIK syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
Traits linked to AP1S1
The Human Phenotype Ontology lists these as features of the rare conditions AP1S1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the digestive system
- Diarrhea
- Abnormality of the intestine
- Impaired release of bile from liver
- Scar tissue replaces healthy tissue in the liver
- Slowed or blocked flow of bile from liver
- Hepatic fibrosis
- Jejunal atresia
- Microcolon
Show 1 more trait
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.). AP1S1 gene: adaptor related protein complex 1 subunit sigma 1. Retrieved 18 October 2026, from https://dantelabs.com/genes/ap1s1
Dante Labs. AP1S1 gene: adaptor related protein complex 1 subunit sigma 1 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/ap1s1
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