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PACS2 phosphofurin acidic cluster sorting protein 2 [ Homo sapiens (human) ]

Gene ID: 23241, updated on 7-Apr-2024

Summary

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Official Symbol
PACS2provided by HGNC
Official Full Name
phosphofurin acidic cluster sorting protein 2provided by HGNC
Primary source
HGNC:HGNC:23794
See related
Ensembl:ENSG00000179364 MIM:610423; AllianceGenome:HGNC:23794
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEE66; EIEE66; PACS-2; PACS1L
Summary
Predicted to enable transmembrane transporter binding activity. Involved in endoplasmic reticulum calcium ion homeostasis; mitochondrion-endoplasmic reticulum membrane tethering; and protein localization to plasma membrane. Acts upstream of or within protein localization to phagophore assembly site. Located in endoplasmic reticulum and mitochondrion. Implicated in developmental and epileptic encephalopathy 66. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 15.4), testis (RPKM 10.2) and 25 other tissues See more
Orthologs
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Genomic context

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See PACS2 in Genome Data Viewer
Location:
14q32.33
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105300774..105398147)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99548161..99645650)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (105767111..105864484)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105658307-105659088 Neighboring gene nudix hydrolase 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105662217-105662998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105662999-105663780 Neighboring gene BRF1 RNA polymerase III transcription initiation factor subunit Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105714496-105715286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105716078-105716867 Neighboring gene BTB domain containing 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105740537-105741440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105749364-105749905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105750449-105750989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105752260-105753158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9144 Neighboring gene uncharacterized LOC124903409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6225 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105778446-105778606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105781451-105782102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105789257-105789766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105794355-105794864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105798394-105799279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105803897-105804562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105804563-105805228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105808627-105809468 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105812556-105812745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105819060-105819589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6230 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105837257-105837460 Neighboring gene ribosomal protein S20 pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105856860-105857360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105857361-105857861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105864965-105865475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105865476-105865986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105877939-105878442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105878443-105878945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105884361-105885030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6237 Neighboring gene testis expressed 22 Neighboring gene MTA1 divergent transcript

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. [Early infantile epileptic encephalopathy caused by PACS2 gene variation: three cases report and literature review]. Wu MJ, et al. Zhonghua Er Ke Za Zhi, 2021 Jul 2. PMID 34405643
  2. Clinical variations of epileptic syndrome associated with PACS2 variant. Mizuno T, et al. Brain Dev, 2021 Feb. PMID 33243487
  3. The Multifunctional Sorting Protein PACS-2 Controls Mitophagosome Formation in Human Vascular Smooth Muscle Cells through Mitochondria-ER Contact Sites. Moulis M, et al. Cells, 2019 Jun 25. PMID 31242668, Free PMC Article
  4. Expanding the clinical spectrum associated with PACS2 mutations. Dentici ML, et al. Clin Genet, 2019 Apr. PMID 30684285
  5. Knockdown of circ_0002194 protects against oxidized low-density lipoprotein-induced cell damage via the regulation of the miR-637/PACS2 axis in human vascular endothelial cells. Mei R, et al. Interact Cardiovasc Thorac Surg, 2022 Sep 9. PMID 35951762, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Characteristics of Developmental and Epileptic Encephalopathy Associated with PACS2 p.Glu209Lys Pathogenic Variant-Our Experience and Systematic Review of the Literature.
    Title: Characteristics of Developmental and Epileptic Encephalopathy Associated with PACS2 p.Glu209Lys Pathogenic Variant-Our Experience and Systematic Review of the Literature.
  2. MAPK1 Mediates MAM Disruption and Mitochondrial Dysfunction in Diabetic Kidney Disease via the PACS-2-Dependent Mechanism.
    Title: MAPK1 Mediates MAM Disruption and Mitochondrial Dysfunction in Diabetic Kidney Disease via the PACS-2-Dependent Mechanism.
  3. Knockdown of circ_0002194 protects against oxidized low-density lipoprotein-induced cell damage via the regulation of the miR-637/PACS2 axis in human vascular endothelial cells.
    Title: Knockdown of circ_0002194 protects against oxidized low-density lipoprotein-induced cell damage via the regulation of the miR-637/PACS2 axis in human vascular endothelial cells.
  4. Clinical variations of epileptic syndrome associated with PACS2 variant.
    Title: Clinical variations of epileptic syndrome associated with PACS2 variant.
  5. [Early infantile epileptic encephalopathy caused by PACS2 gene variation: three cases report and literature review].
    Title: [Early infantile epileptic encephalopathy caused by PACS2 gene variation: three cases report and literature review].
  6. Coloboma may be a shared feature in a spectrum of disorders caused by mutations in the WDR37-PACS1-PACS2 axis.
    Title: Coloboma may be a shared feature in a spectrum of disorders caused by mutations in the WDR37-PACS1-PACS2 axis.
  7. These findings confirmed our previous research and expanded the mutational spectrum of WEE2, making it a potential genetic diagnostic marker for those suffering from human fertilization failure.
    Title: Expanding the clinical spectrum associated with PACS2 mutations.
  8. the role of the multifunctional Mitochondria-associated endoplasmic reticulum membrane protein phosphofurin acidic cluster sorting protein 2 (PACS-2) in regulating Vascular Smooth Muscle Cell survival following a challenge by atherogenic lipids.
    Title: The Multifunctional Sorting Protein PACS-2 Controls Mitophagosome Formation in Human Vascular Smooth Muscle Cells through Mitochondria-ER Contact Sites.
  9. Insulin acutely regulates SIRT1 activity by triggering recruitment of PACS-2 and DBC1 to the SIRT1 N terminal region creating a regulatory hub.
    Title: An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity.
  10. These findings support the causality of this recurrent de novo PACS2 heterozygous missense in Developmental and epileptic encephalopathies with facial dysmorphim and cerebellar dysgenesis.
    Title: A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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

Associated conditions

Description Tests
Developmental and epileptic encephalopathy, 66
MedGen: C4748070 OMIM: 618067 GeneReviews: Not available
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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Amino-acid residues 102-116 in the FBR region of PACS-2 bind to HIV-1 Nef and alanine-scanning analysis reveals that amino acid N109 is required for the binding between PACS-2 and Nef PubMed
nef HIV-1 Nef-mediated downregulation of MHC-I requires Nef motif EEEE(65)-dependent binding to the sorting protein PACS-2, which targets Nef to the paranuclear region and enables Nef PXXP(75) to bind and activate a trans-Golgi network localized Src kinase PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25488, KIAA0602

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane transporter binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within autophagosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endoplasmic reticulum calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrion-endoplasmic reticulum membrane tethering IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within protein localization to phagophore assembly site IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein localization to plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
phosphofurin acidic cluster sorting protein 2
Names
PACS1-like protein

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001100913.3 → NP_001094383.2  phosphofurin acidic cluster sorting protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001094383.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB011174, AL928654, CA423467
    Consensus CDS
    CCDS45178.2
    UniProtKB/TrEMBL
    F8VW41
    Related
    ENSP00000393559.2, ENST00000447393.6
    Conserved Domains (1) summary
    pfam10254
    Location:477 → 900
    Pacs-1; PACS-1 cytosolic sorting protein

  2. NM_001243127.3 → NP_001230056.1  phosphofurin acidic cluster sorting protein 2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, uses an alternate in-frame splice site in the central coding region, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK098354, AL512355, BC065220, BC131591, CA423467, DA177001, DA408379, HY009105
    Consensus CDS
    CCDS58339.1
    UniProtKB/TrEMBL
    F8VW41
    Related
    ENSP00000393524.2, ENST00000430725.6
    Conserved Domains (1) summary
    pfam10254
    Location:398 → 810
    Pacs-1; PACS-1 cytosolic sorting protein

  3. NM_015197.4 → NP_056012.2  phosphofurin acidic cluster sorting protein 2 isoform 2

    See identical proteins and their annotated locations for NP_056012.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AL512355, AL928654, BC065220, CA423467
    Consensus CDS
    CCDS32168.1
    UniProtKB/Swiss-Prot
    A2VDJ9, G8JLK3, O60342, Q6P191, Q86VP3, Q96FL7
    UniProtKB/TrEMBL
    F8VW41
    Related
    ENSP00000321834.8, ENST00000325438.12
    Conserved Domains (1) summary
    pfam10254
    Location:473 → 885
    Pacs-1; PACS-1 cytosolic sorting protein

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
    105300774..105398147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021112.3 → XP_016876601.1  phosphofurin acidic cluster sorting protein 2 isoform X12

    UniProtKB/TrEMBL
    F8VW41

  2. XM_017021111.3 → XP_016876600.1  phosphofurin acidic cluster sorting protein 2 isoform X13

    UniProtKB/TrEMBL
    F8VW41

  3. XM_006720090.3 → XP_006720153.1  phosphofurin acidic cluster sorting protein 2 isoform X1

    UniProtKB/TrEMBL
    F8VW41
    Conserved Domains (1) summary
    pfam10254
    Location:478 → 901
    Pacs-1; PACS-1 cytosolic sorting protein

  4. XM_006720091.3 → XP_006720154.1  phosphofurin acidic cluster sorting protein 2 isoform X6

    UniProtKB/TrEMBL
    F8VW41
    Conserved Domains (1) summary
    pfam10254
    Location:478 → 890
    Pacs-1; PACS-1 cytosolic sorting protein

  5. XM_017021105.3 → XP_016876594.1  phosphofurin acidic cluster sorting protein 2 isoform X2

    UniProtKB/TrEMBL
    F8VW41

  6. XM_017021110.3 → XP_016876599.1  phosphofurin acidic cluster sorting protein 2 isoform X9

    UniProtKB/TrEMBL
    F8VW41

  7. XM_017021109.3 → XP_016876598.1  phosphofurin acidic cluster sorting protein 2 isoform X7

    UniProtKB/TrEMBL
    F8VW41

  8. XM_017021106.3 → XP_016876595.1  phosphofurin acidic cluster sorting protein 2 isoform X3

    UniProtKB/TrEMBL
    F8VW41

  9. XM_017021107.3 → XP_016876596.1  phosphofurin acidic cluster sorting protein 2 isoform X4

    UniProtKB/TrEMBL
    F8VW41

  10. XM_047431164.1 → XP_047287120.1  phosphofurin acidic cluster sorting protein 2 isoform X10

  11. XM_017021108.3 → XP_016876597.1  phosphofurin acidic cluster sorting protein 2 isoform X5

    UniProtKB/TrEMBL
    F8VW41

  12. XM_047431163.1 → XP_047287119.1  phosphofurin acidic cluster sorting protein 2 isoform X8

  13. XM_006720092.4 → XP_006720155.1  phosphofurin acidic cluster sorting protein 2 isoform X11

    UniProtKB/TrEMBL
    F8VW41
    Conserved Domains (1) summary
    pfam10254
    Location:465 → 877
    Pacs-1; PACS-1 cytosolic sorting protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99548161..99645650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375707.1 → XP_054231682.1  phosphofurin acidic cluster sorting protein 2 isoform X12

  2. XM_054375708.1 → XP_054231683.1  phosphofurin acidic cluster sorting protein 2 isoform X13

  3. XM_054375696.1 → XP_054231671.1  phosphofurin acidic cluster sorting protein 2 isoform X1

  4. XM_054375701.1 → XP_054231676.1  phosphofurin acidic cluster sorting protein 2 isoform X6

  5. XM_054375697.1 → XP_054231672.1  phosphofurin acidic cluster sorting protein 2 isoform X2

  6. XM_054375704.1 → XP_054231679.1  phosphofurin acidic cluster sorting protein 2 isoform X9

  7. XM_054375702.1 → XP_054231677.1  phosphofurin acidic cluster sorting protein 2 isoform X7

  8. XM_054375698.1 → XP_054231673.1  phosphofurin acidic cluster sorting protein 2 isoform X3

  9. XM_054375699.1 → XP_054231674.1  phosphofurin acidic cluster sorting protein 2 isoform X4

  10. XM_054375705.1 → XP_054231680.1  phosphofurin acidic cluster sorting protein 2 isoform X10

  11. XM_054375700.1 → XP_054231675.1  phosphofurin acidic cluster sorting protein 2 isoform X5

  12. XM_054375703.1 → XP_054231678.1  phosphofurin acidic cluster sorting protein 2 isoform X8

  13. XM_054375706.1 → XP_054231681.1  phosphofurin acidic cluster sorting protein 2 isoform X11

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86VP3.3 GenPept UniProtKB/Swiss-Prot:Q86VP3

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