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    PHACTR2 phosphatase and actin regulator 2 [ Homo sapiens (human) ]

    Gene ID: 9749, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PHACTR2provided by HGNC
    Official Full Name
    phosphatase and actin regulator 2provided by HGNC
    Primary source
    HGNC:HGNC:20956
    See related
    Ensembl:ENSG00000112419 MIM:608724; AllianceGenome:HGNC:20956
    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
    C6orf56
    Summary
    Predicted to enable actin binding activity. Predicted to be involved in actin cytoskeleton organization. Predicted to be located in plasma membrane and platelet alpha granule membrane. Implicated in Parkinson's disease and multiple sclerosis. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in placenta (RPKM 29.1), adrenal (RPKM 11.9) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHACTR2 in Genome Data Viewer
    Location:
    6q24.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (143536878..143831185)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (144729279..145023866)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (143858015..144152322)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901417 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:143832090-143832293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143832494-143833156 Neighboring gene uncharacterized LOC105378035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143833157-143833817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17629 Neighboring gene alpha-L-fucosidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25203 Neighboring gene PHACTR2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17630 Neighboring gene MPRA-validated peak6177 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:143958702-143959245 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:143998446-143999294 Neighboring gene MPRA-validated peak6179 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144059920-144060420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144065167-144065836 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144067178-144067848 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144067849-144068518 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144068519-144069188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25206 Neighboring gene MPRA-validated peak6180 silencer Neighboring gene MPRA-validated peak6181 silencer Neighboring gene LTV1 ribosome biogenesis factor Neighboring gene zinc finger C2HC-type containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25207

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. rs9390123 and rs9399451 influence the DNA repair capacity of lung cancer by regulating PEX3 and PHACTR2AS1 expression instead of PHACTR2.
      Title: rs9390123 and rs9399451 influence the DNA repair capacity of lung cancer by regulating PEX3 and PHACTR2‑AS1 expression instead of PHACTR2.
    2. The frequencies of genotype and allele in CHRNA3 (rs8040868) and PHACTR2 (rs9390123) were not significantly different between the NSCLC cases and controls, or between either of the subgroups.
      Title: Association between polymorphisms in CHRNA3 and PHACTR2 gene and environment and NSCLC risk in Chinese population.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. identified an association between Phactr2 SNP rs11155313 and Parkinson's disease in US, Canadian and Irish patient populations, but not in a Norwegian population
      Title: Phactr2 and Parkinson's disease.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study reveals novel genetic determinants of DNA repair capacity in lung cancer.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Pilot genome-wide association search identifies potential loci for risk of erectile dysfunction in type 1 diabetes using the DCCT/EDIC study cohort.
    EBI GWAS Catalog

    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
    Vif vif HIV-1 Vif downregulates the expression of phosphatase and actin regulator 2 (PHACTR2) in Vif-expression T cells 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

    • KIAA0680, MGC176642, DKFZp686F18175

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in platelet alpha granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    phosphatase and actin regulator 2

    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.

    mRNA and Protein(s)

    1. NM_001100164.2 → NP_001093634.1  phosphatase and actin regulator 2 isoform 1

      See identical proteins and their annotated locations for NP_001093634.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB014580, AL049844, CN361694, DC361499, DR980875
      Consensus CDS
      CCDS47493.1
      UniProtKB/Swiss-Prot
      O75167
      Related
      ENSP00000417038.2, ENST00000440869.7
      Conserved Domains (2) summary
      smart00707
      Location:527 → 551
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      pfam02755
      Location:72 → 94
      RPEL; RPEL repeat

    2. NM_001100165.2 → NP_001093635.1  phosphatase and actin regulator 2 isoform 2

      See identical proteins and their annotated locations for NP_001093635.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AB014580, AL049844, DC361499, DR004592, DR980875
      Consensus CDS
      CCDS47494.1
      UniProtKB/Swiss-Prot
      O75167
      Related
      ENSP00000356554.3, ENST00000367582.7
      Conserved Domains (2) summary
      smart00707
      Location:447 → 471
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      pfam02755
      Location:72 → 94
      RPEL; RPEL repeat

    3. NM_001100166.2 → NP_001093636.1  phosphatase and actin regulator 2 isoform 4

      See identical proteins and their annotated locations for NP_001093636.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, has multiple differences in the presence and absence of exons at its 5' end, and lacks an alternate in-frame exon in the mid-coding region, compared to variant 1. The resulting protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB014580, AL049844, DC381966, DN993504, DR980875
      Consensus CDS
      CCDS43512.1
      UniProtKB/Swiss-Prot
      O75167
      Related
      ENSP00000305530.6, ENST00000305766.10
      Conserved Domains (2) summary
      smart00707
      Location:436 → 460
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      pfam02755
      Location:61 → 83
      RPEL; RPEL repeat

    4. NM_001394736.1 → NP_001381665.1  phosphatase and actin regulator 2 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL049844, AL078593, AL357117
      Consensus CDS
      CCDS94015.1
      UniProtKB/TrEMBL
      J3KP75
      Related
      ENSP00000356556.4, ENST00000367584.8
      Conserved Domains (1) summary
      smart00707
      Location:504 → 528
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    5. NM_001394738.1 → NP_001381667.1  phosphatase and actin regulator 2 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL049844, AL078593, AL357117
      Conserved Domains (2) summary
      smart00707
      Location:383 → 407
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      cl29414
      Location:344 → 369
      RPEL; RPEL repeat

    6. NM_014721.3 → NP_055536.2  phosphatase and actin regulator 2 isoform 3

      See identical proteins and their annotated locations for NP_055536.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, and has multiple differences in the presence and absence of exons at its 5' end, compared to variant 1. The resulting protein (isoform 3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB014580, AL049844, CN361694, DC381966, DR980875
      Consensus CDS
      CCDS47492.1
      UniProtKB/Swiss-Prot
      A6NKP5, A7MCZ5, A8MZC0, B2RWP7, B4DN76, B4DPB5, B4DTH7, O75167, Q5TFA0, Q68DM2
      Related
      ENSP00000391763.2, ENST00000427704.6
      Conserved Domains (2) summary
      smart00707
      Location:516 → 540
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      pfam02755
      Location:61 → 83
      RPEL; RPEL repeat

    RNA

    1. NR_172204.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL049844, AL078593, AL357117

    2. NR_172205.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL049844, AL078593, AL360228

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      143536878..143831185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      144729279..145023866
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75167.2 GenPept UniProtKB/Swiss-Prot:O75167

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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