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

    Gene ID: 23241, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 15.4), testis (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105300774..105398147)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99548161..99645650)
    RS_2024_09 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 general transcription factor IIIB 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Characteristics of Developmental and Epileptic Encephalopathy Associated with PACS2 p.Glu209Lys Pathogenic Variant-Our Experience and Systematic Review of the Literature. Stoian A, et al. Biomolecules, 2024 Feb 23. PMID 38540691, Free PMC Article
    2. [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
    3. Clinical variations of epileptic syndrome associated with PACS2 variant. Mizuno T, et al. Brain Dev, 2021 Feb. PMID 33243487
    4. 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
    5. Expanding the clinical spectrum associated with PACS2 mutations. Dentici ML, et al. Clin Genet, 2019 Apr. PMID 30684285

    See all (38) 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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_2024_08

    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

      UniProtKB/TrEMBL
      F8VW41

    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

      UniProtKB/TrEMBL
      F8VW41

    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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41

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

      UniProtKB/TrEMBL
      F8VW41
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VP3.3 GenPept UniProtKB/Swiss-Prot:Q86VP3

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