AP2S1

protein-coding

adaptor related protein complex 2 subunit sigma 1, the group of Adaptor related protein complex 2

Gene summary

One of two major clathrin-associated adaptor complexes, AP-2, is a heterotetramer which is associated with the plasma membrane. This complex is composed of two large chains, a medium chain, and a small chain. This gene encodes the small chain of this complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

Previous symbols:
  • CLAPS2
  • HHC3

MANE transcript

NM_004069.6

Inheritance

AD

ClinVar variants

P:4U:31B:35

Top phenotype

Hypocalciuric hypercalcemia, familial, type III

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr19:46,838,136-46,850,846

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~12.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

familial hypocalciuric hypercalcemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010926

Submitter: PanelApp Australia

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: G2P

familial hypocalciuric hypercalcemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010926

Submitter: Ambry Genetics

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

autism spectrum disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005258

Submitter: Ambry Genetics

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

familial hypocalciuric hypercalcemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010926

Submitter: Labcorp Genetics (formerly Invitae)

familial hypocalciuric hypercalcemia 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010926

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Hypocalciuric hypercalcemia, familial, type IIIAD

Manifestation: Endocrine

Intervention: Endocrine

Rationale: The condition can involve parathyroidectomy-refractory sequelae of hypercalcemia such as headaches, fatigue, and pain, and medical treatment (eg, with cinacalcet) has been reported as benefical related to symptoms as well as biochemical parameters

Refs: 23222959; 27050234Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AP2S1 variants in ClinVar

12 Conditions Cataloged
not providedTotal: 103
not specifiedTotal: 21
Familial hypocalciuric hypercalcemia 3Total: 16
AP2S1-related disorderTotal: 8
Inborn genetic diseasesTotal: 7
AP2S1-associated neurodevelopmental diseaseTotal: 1
Neurodevelopmental disorderTotal: 1
AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004069.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
35
clinvar
35
missense
2
clinvar
2
clinvar
30
clinvar
34
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total223135070

Highest pathogenic variant AF is 0.0000020521463

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004069.6RefSeqNP_004060.25MANE Select
ENST00000263270.11EnsemblENSP00000263270.65MANE Select
NM_001301076.3RefSeqNP_001288005.15Standard
NM_001301078.3RefSeqNP_001288007.15Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Synaptic vesicle cycle - Homo sapiens (human)
  • Endocytosis - Homo sapiens (human)
  • Huntington,s disease - Homo sapiens (human)
  • Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human)
  • Synaptic Vesicle Pathway

Biological Process

  • intracellular protein transport
  • antigen processing and presentation of exogenous peptide antigen via MHC class II
  • regulation of endocytosis
  • low-density lipoprotein particle receptor catabolic process
  • low-density lipoprotein particle clearance

Molecular Function

  • transporter activity
  • protein binding
  • protein transporter activity
  • clathrin adaptor activity

Cellular Component

  • cytosol
  • plasma membrane
  • AP-2 adaptor complex
  • endocytic vesicle membrane
  • clathrin-coated endocytic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000263270
Coding exons
5
Length
12857
Individuals with no LoFs
125745
Homozygous LoFs
0
Heterozygous LoFs
1
Defined
125746
p
0.00000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.861592.40.1620.00000615942
Missense (PolyPhen)036.110432
Synonymous0.05823939.50.9880.00000270261
Loss of Function2.5519.440.1065.72e-793

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Component of the adaptor protein complex 2 (AP-2). Adaptor protein complexes function in protein Transport via Transport vesicles in different membrane traffic pathways. Adaptor protein complexes are vesicle coat components and appear to be involved in cargo selection and vesicle formation. AP-2 is involved in clathrin-dependent endocytosis in which cargo proteins are incorporated into vesicles surrounded by clathrin (clathrin- coated vesicles, CCVs) which are destined for fusion with the early endosome. The clathrin lattice serves as a mechanical scaffold but is itself unable to bind directly to membrane components. Clathrin-associated adaptor protein (AP) complexes which can bind directly to both the clathrin lattice and to the lipid and protein components of membranes are considered to be the major clathrin adaptors contributing the CCV formation. AP-2 also serves as a cargo receptor to selectively sort the membrane proteins involved in receptor-mediated endocytosis. AP-2 seems to play a role in the recycling of synaptic vesicle membranes from the presynaptic surface. AP-2 recognizes Y-X-X-[FILMV] (Y-X-X-Phi) and [ED]-X-X-X-L-[LI] endocytosis signal motifs within the cytosolic tails of transmembrane cargo molecules. AP-2 may also play a role in maintaining normal post-endocytic trafficking through the ARF6-regulated, non-clathrin pathway. The AP-2 alpha and AP-2 sigma subunits are thought to contribute to the recognition of the [ED]-X-X-X-L-[LI] motif (By similarity). May also play a role in extracellular calcium homeostasis. {ECO:0000250, ECO:0000269|PubMed:14745134, ECO:0000269|PubMed:15473838, ECO:0000269|PubMed:19033387, ECO:0000269|PubMed:23222959}.;
Disease
DISEASE: Hypocalciuric hypercalcemia, familial 3 (HHC3) [MIM:600740]: A form of hypocalciuric hypercalcemia, a disorder of mineral homeostasis that is transmitted as an autosomal dominant trait with a high degree of penetrance. It is characterized biochemically by lifelong elevation of serum calcium concentrations and is associated with inappropriately low urinary calcium excretion and a normal or mildly elevated circulating parathyroid hormone level. Hypermagnesemia is typically present. Affected individuals are usually asymptomatic and the disorder is considered benign. However, chondrocalcinosis and pancreatitis occur in some adults. {ECO:0000269|PubMed:23222959, ECO:0000269|PubMed:24081735}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.163

Intolerance Scores

LoFtool
0.186
RVIS EVS
0.01
RVIS percentile EVS
54.63

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
S
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.965

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow
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