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AP4S1 adaptor related protein complex 4 subunit sigma 1 [ Homo sapiens (human) ]

Gene ID: 11154, updated on 5-Mar-2024

Summary

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Official Symbol
AP4S1provided by HGNC
Official Full Name
adaptor related protein complex 4 subunit sigma 1provided by HGNC
Primary source
HGNC:HGNC:575
See related
Ensembl:ENSG00000100478 MIM:607243; AllianceGenome:HGNC:575
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AP47B; CLA20; CPSQ6; SPG52; CLAPS4
Summary
This gene encodes a member of the adaptor complexes small subunit protein family. These proteins are components of the heterotetrameric adaptor protein complexes, which play important roles in the secretory and endocytic pathways by mediating vesicle formation and sorting of integral membrane proteins. The encoded protein is the small subunit of adaptor protein complex-4, which is associated with both clathrin- and nonclathrin-coated vesicles. Mutations in this gene are associated with spastic quadriplegic cerebral palsy-6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 6. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in brain (RPKM 1.8), testis (RPKM 1.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (31025106..31096450)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (25222939..25294259)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31494312..31565656)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene striatin 3 Neighboring gene intraflagellar transport 20 homolog (Chlamydomonas) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8228 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:31494803-31494984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8229 Neighboring gene microRNA 624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:31516497-31517022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5652 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:31591905-31592742 Neighboring gene HECT domain E3 ubiquitin protein ligase 1 Neighboring gene ribosomal protein L21 pseudogene 5 Neighboring gene RNA, U6 small nuclear 541, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia. McCullough CG, et al. Hum Mutat, 2020 Feb. PMID 31660686
  2. Identification of mutations in AP4S1/SPG52 through next generation sequencing in three families. Tessa A, et al. Eur J Neurol, 2016 Oct. PMID 27444738
  3. Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly. Hardies K, et al. Hum Mol Genet, 2015 Apr 15. PMID 25552650, Free PMC Article
  4. AP-4-Associated Hereditary Spastic Paraplegia. Adam MP, et al. , 1993. PMID 30543385
  5. Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature. Abou Jamra R, et al. Am J Hum Genet, 2011 Jun 10. PMID 21620353, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia.
    Title: Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia.
  2. Loss of ap4s1 in zebrafish leads to neurodevelopmental defects resembling spastic paraplegia 52.
    Title: Loss of ap4s1 in zebrafish leads to neurodevelopmental defects resembling spastic paraplegia 52.
  3. Identification of mutations in AP4S1/SPG52 in hereditary spastic paraplegia.
    Title: Identification of mutations in AP4S1/SPG52 through next generation sequencing in three families.
  4. Premature stop mutations in AP4S1 result in loss of AP-4 complex assembly and cause fever-sensitive seizures, developmental delay and spastic paraplegia.
    Title: Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ32366, FLJ41011

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in protein localization IC
Inferred by Curator
more info
 PubMed 
involved_in protein targeting IC
Inferred by Curator
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of AP-4 adaptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of AP-4 adaptor complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endosome lumen TAS
Traceable Author Statement
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in trans-Golgi network NAS
Non-traceable Author Statement
more info
 PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
AP-4 complex subunit sigma-1
Names
AP-4 adapter complex subunit sigma-1
AP-4 adaptor complex subunit sigma-1
adaptor related protein complex 4 sigma 1 subunit
clathrin-associated/assembly/adaptor protein, sigma 4
sigma-4-adaptin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031913.1 RefSeqGene

    Range
    5544..76345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001128126.3 → NP_001121598.1  AP-4 complex subunit sigma-1 isoform 2

    See identical proteins and their annotated locations for NP_001121598.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI570549, AK304115, AL121808, R46468
    Consensus CDS
    CCDS45093.1
    UniProtKB/Swiss-Prot
    G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
    UniProtKB/TrEMBL
    B7ZB52
    Related
    ENSP00000438170.2, ENST00000542754.7
    Conserved Domains (1) summary
    cd14832
    Location:3 → 140
    AP4_sigma; AP-4 complex subunit sigma

  2. NM_001254726.2 → NP_001241655.1  AP-4 complex subunit sigma-1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AL121808, BC001259, BG702035, BX388185
    Consensus CDS
    CCDS58310.1
    UniProtKB/Swiss-Prot
    Q9Y587
    Related
    ENSP00000452383.2, ENST00000554609.6
    Conserved Domains (1) summary
    cl02092
    Location:1 → 102
    Clat_adaptor_s; Clathrin adaptor complex small chain

  3. NM_001254727.2 → NP_001241656.1  AP-4 complex subunit sigma-1 isoform 4

    See identical proteins and their annotated locations for NP_001241656.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate internal exon, which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL121808, BC001259, BG702035, BX247969
    Consensus CDS
    CCDS58309.1
    UniProtKB/TrEMBL
    A0A5F9ZH42
    Related
    ENSP00000334484.4, ENST00000334725.8
    Conserved Domains (2) summary
    cl02092
    Location:1 → 105
    Clat_adaptor_s; Clathrin adaptor complex small chain
    pfam13900
    Location:128 → 149
    GVQW; Putative domain of unknown function

  4. NM_001254728.2 → NP_001241657.1  AP-4 complex subunit sigma-1 isoform 2

    See identical proteins and their annotated locations for NP_001241657.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI570549, AL121808, BC035622, R46468
    Consensus CDS
    CCDS45093.1
    UniProtKB/Swiss-Prot
    G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
    UniProtKB/TrEMBL
    B7ZB52
    Related
    ENSP00000451609.2, ENST00000555417.6
    Conserved Domains (1) summary
    cd14832
    Location:3 → 140
    AP4_sigma; AP-4 complex subunit sigma

  5. NM_001254729.2 → NP_001241658.1  AP-4 complex subunit sigma-1 isoform 2

    See identical proteins and their annotated locations for NP_001241658.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI570549, AK304115, AL049830, AL121808, BF671561, R46468
    Consensus CDS
    CCDS45093.1
    UniProtKB/Swiss-Prot
    G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
    UniProtKB/TrEMBL
    B7ZB52
    Related
    ENSP00000451479.2, ENST00000557346.6
    Conserved Domains (1) summary
    cd14832
    Location:3 → 140
    AP4_sigma; AP-4 complex subunit sigma

  6. NM_007077.5 → NP_009008.2  AP-4 complex subunit sigma-1 isoform 1

    See identical proteins and their annotated locations for NP_009008.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL121808, BC001259, BG702035
    Consensus CDS
    CCDS9642.1
    UniProtKB/Swiss-Prot
    Q9Y587
    Related
    ENSP00000450768.2, ENST00000554345.6
    Conserved Domains (1) summary
    cl02092
    Location:1 → 105
    Clat_adaptor_s; Clathrin adaptor complex small chain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    31025106..31096450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536371.4 → XP_011534673.1  AP-4 complex subunit sigma-1 isoform X1

    See identical proteins and their annotated locations for XP_011534673.1

    UniProtKB/Swiss-Prot
    Q9Y587
    Conserved Domains (1) summary
    cl02092
    Location:1 → 105
    Clat_adaptor_s; Clathrin adaptor complex small chain

  2. XM_005267293.6 → XP_005267350.1  AP-4 complex subunit sigma-1 isoform X1

    See identical proteins and their annotated locations for XP_005267350.1

    UniProtKB/Swiss-Prot
    Q9Y587
    Conserved Domains (1) summary
    cl02092
    Location:1 → 105
    Clat_adaptor_s; Clathrin adaptor complex small chain

  3. XM_011536372.4 → XP_011534674.1  AP-4 complex subunit sigma-1 isoform X1

    See identical proteins and their annotated locations for XP_011534674.1

    UniProtKB/Swiss-Prot
    Q9Y587
    Conserved Domains (1) summary
    cl02092
    Location:1 → 105
    Clat_adaptor_s; Clathrin adaptor complex small chain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    25222939..25294259
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375291.1 → XP_054231266.1  AP-4 complex subunit sigma-1 isoform X1

  2. XM_054375292.1 → XP_054231267.1  AP-4 complex subunit sigma-1 isoform X1

  3. XM_054375293.1 → XP_054231268.1  AP-4 complex subunit sigma-1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y587.1 GenPept UniProtKB/Swiss-Prot:Q9Y587

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