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    PSD3 pleckstrin and Sec7 domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 23362, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PSD3provided by HGNC
    Official Full Name
    pleckstrin and Sec7 domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:19093
    See related
    Ensembl:ENSG00000156011 MIM:614440; AllianceGenome:HGNC:19093
    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
    EFA6D; EFA6R; HCA67
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse; postsynapse; and ruffle membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 17.3), adrenal (RPKM 6.3) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PSD3 in Genome Data Viewer
    Location:
    8p22
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (18527303..19084805, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (18794850..19349609, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (18384813..18942315, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L10a pseudogene 11 Neighboring gene N-acetyltransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:18372869-18373421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:18394809-18395372 Neighboring gene uncharacterized LOC124901896 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:18473110-18473654 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:18522753-18523952 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:18536540-18537102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27053 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:18624592-18625402 Neighboring gene Sharpr-MPRA regulatory region 772 Neighboring gene ribosomal protein L35 pseudogene 6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:18696773-18697972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:18703980-18704480 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:18704481-18704981 Neighboring gene uncharacterized LOC124901897 Neighboring gene uncharacterized LOC124901895 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:18761786-18762609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:18771177-18771688 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:18797082-18798281 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:18819125-18819328 Neighboring gene uncharacterized LOC107986868 Neighboring gene small nucleolar RNA SNORA62/SNORA6 family Neighboring gene uncharacterized LOC105379303 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:18859165-18859442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18967 Neighboring gene uncharacterized LOC124901898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:18941277-18942070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:18942071-18942864 Neighboring gene uncharacterized LOC105379301 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:19034764-19035693 Neighboring gene uncharacterized LOC100128993 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:19051482-19052681 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:19068899-19069055 Neighboring gene ATPase plasma membrane Ca2+ transporting 1 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 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. Genetic association analysis of polymorphisms in PSD3 gene with obesity, type 2 diabetes, and HDL cholesterol. Gong S, et al. Diabetes Res Clin Pract, 2017 Apr. PMID 28237857
    2. PSD3 downregulation confers protection against fatty liver disease. Mancina RM, et al. Nat Metab, 2022 Jan. PMID 35102341, Free PMC Article
    3. Exchange factor EFA6R requires C-terminal targeting to the plasma membrane to promote cytoskeletal rearrangement through the activation of ADP-ribosylation factor 6 (ARF6). Kanamarlapudi V. J Biol Chem, 2014 Nov 28. PMID 25296758, Free PMC Article
    4. Genome-wide association study of urinary albumin excretion rate in patients with type 1 diabetes. Sandholm N, et al. Diabetologia, 2014 Jun. PMID 24595857
    5. Five genes from chromosomal band 8p22 are significantly down-regulated in ovarian carcinoma: N33 and EFA6R have a potential impact on overall survival. Pils D, et al. Cancer, 2005 Dec 1. PMID 16270321

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PSD3 downregulation confers protection against fatty liver disease.
      Title: PSD3 downregulation confers protection against fatty liver disease.
    2. Common variants in PSD3 were associated with obesity, T2D and HDL level
      Title: Genetic association analysis of polymorphisms in PSD3 gene with obesity, type 2 diabetes, and HDL cholesterol.
    3. EFA6R regulated ARF6 localization and thereby actin stress fiber loss.
      Title: Exchange factor EFA6R requires C-terminal targeting to the plasma membrane to promote cytoskeletal rearrangement through the activation of ADP-ribosylation factor 6 (ARF6).
    4. 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.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Inherited genetic variant predisposes to aggressive but not indolent prostate cancer.
    6. Down regulated in ovarian cancer or absent in ovarian cancer and impact survival.
      Title: Five genes from chromosomal band 8p22 are significantly down-regulated in ovarian carcinoma: N33 and EFA6R have a potential impact on overall survival.
    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2016-12-07)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2016-12-07)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
    EBI GWAS Catalog
    Gene network analysis in a pediatric cohort identifies novel lung function genes.
    EBI GWAS Catalog
    Genome-wide association study identifies ephrin type A receptors implicated in paclitaxel induced peripheral sensory neuropathy.
    EBI GWAS Catalog
    Genome-wide association study of urinary albumin excretion rate in patients with type 1 diabetes.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp761K1423

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in ruffle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ruffle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    PH and SEC7 domain-containing protein 3
    Names
    ADP-ribosylation factor guanine nucleotide factor 6
    epididymis tissue protein Li 20mP
    exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 D
    exchange factor for ARF6 D
    hepatocellular carcinoma-associated antigen 67
    pleckstrin homology and SEC7 domain-containing protein 3

    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_001362819.2 → NP_001349748.1  PH and SEC7 domain-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC120051, AF243495, AK091317
      UniProtKB/Swiss-Prot
      A6NFQ4, E9KL50, Q6B003, Q9NYI0, Q9Y2F1
      Conserved Domains (2) summary
      cd00171
      Location:548 → 702
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:747 → 872
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    2. NM_001412865.1 → NP_001399794.1  PH and SEC7 domain-containing protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC100849, AC120051

    3. NM_001412866.1 → NP_001399795.1  PH and SEC7 domain-containing protein 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC100849, AC120051

    4. NM_001412867.1 → NP_001399796.1  PH and SEC7 domain-containing protein 3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100849

    5. NM_001412868.1 → NP_001399797.1  PH and SEC7 domain-containing protein 3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100849

    6. NM_001412869.1 → NP_001399798.1  PH and SEC7 domain-containing protein 3 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100849

    7. NM_001412870.1 → NP_001399799.1  PH and SEC7 domain-containing protein 3 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    8. NM_001412871.1 → NP_001399800.1  PH and SEC7 domain-containing protein 3 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    9. NM_001412872.1 → NP_001399801.1  PH and SEC7 domain-containing protein 3 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    10. NM_001412873.1 → NP_001399802.1  PH and SEC7 domain-containing protein 3 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    11. NM_001412874.1 → NP_001399803.1  PH and SEC7 domain-containing protein 3 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051
      UniProtKB/TrEMBL
      E5RJ29

    12. NM_001412875.1 → NP_001399804.1  PH and SEC7 domain-containing protein 3 isoform 14

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    13. NM_001412876.1 → NP_001399805.1  PH and SEC7 domain-containing protein 3 isoform 15

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051

    14. NM_001412877.1 → NP_001399806.1  PH and SEC7 domain-containing protein 3 isoform 16

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420

    15. NM_001412879.1 → NP_001399808.1  PH and SEC7 domain-containing protein 3 isoform 17

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420

    16. NM_001412880.1 → NP_001399809.1  PH and SEC7 domain-containing protein 3 isoform 18

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800

    17. NM_001412881.1 → NP_001399810.1  PH and SEC7 domain-containing protein 3 isoform 19

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420

    18. NM_001412882.1 → NP_001399811.1  PH and SEC7 domain-containing protein 3 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC009884, AC087821, AC090420, AC100800, AC120051
      UniProtKB/TrEMBL
      E5RJ29

    19. NM_001412883.1 → NP_001399812.1  PH and SEC7 domain-containing protein 3 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051
      UniProtKB/TrEMBL
      E5RJ29
      Related
      ENSP00000430640.1, ENST00000523619.5

    20. NM_001412884.1 → NP_001399813.1  PH and SEC7 domain-containing protein 3 isoform 20

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420
      Related
      ENSP00000430744.1, ENST00000520858.5

    21. NM_001412885.1 → NP_001399814.1  PH and SEC7 domain-containing protein 3 isoform 21

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051

    22. NM_001412886.1 → NP_001399815.1  PH and SEC7 domain-containing protein 3 isoform 21

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051

    23. NM_001412887.1 → NP_001399816.1  PH and SEC7 domain-containing protein 3 isoform 22

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420

    24. NM_001412888.1 → NP_001399817.1  PH and SEC7 domain-containing protein 3 isoform 21

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051

    25. NM_001412889.1 → NP_001399818.1  PH and SEC7 domain-containing protein 3 isoform 21

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051

    26. NM_001412890.1 → NP_001399819.1  PH and SEC7 domain-containing protein 3 isoform 23

      Status: VALIDATED

      Source sequence(s)
      AC087821, AC090420, AC100800, AC120051

    27. NM_001412891.1 → NP_001399820.1  PH and SEC7 domain-containing protein 3 isoform 30

      Status: VALIDATED

      Source sequence(s)
      AC090420, AC100800, AC120051

    28. NM_001412892.1 → NP_001399821.1  PH and SEC7 domain-containing protein 3 isoform 25

      Status: VALIDATED

      Source sequence(s)
      AC090420
      Related
      ENST00000518963.5

    29. NM_001412893.1 → NP_001399822.1  PH and SEC7 domain-containing protein 3 isoform 26

      Status: VALIDATED

      Source sequence(s)
      AC090420

    30. NM_001412894.1 → NP_001399823.1  PH and SEC7 domain-containing protein 3 isoform 27

      Status: VALIDATED

      Source sequence(s)
      AC090420

    31. NM_001412895.1 → NP_001399824.1  PH and SEC7 domain-containing protein 3 isoform 28

      Status: VALIDATED

      Source sequence(s)
      AC100800, AC120051
      UniProtKB/TrEMBL
      B4DKF8
      Related
      ENSP00000393228.2, ENST00000428502.6

    32. NM_001412896.1 → NP_001399825.1  PH and SEC7 domain-containing protein 3 isoform 29

      Status: VALIDATED

      Source sequence(s)
      AC100800, AC120051

    33. NM_015310.4 → NP_056125.3  PH and SEC7 domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_056125.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC009884, AC087821, AC120051, AF243495, AK091317
      Consensus CDS
      CCDS43720.1
      UniProtKB/Swiss-Prot
      A6NFQ4, E9KL50, Q6B003, Q9NYI0, Q9Y2F1
      Related
      ENSP00000324127.8, ENST00000327040.13
      Conserved Domains (3) summary
      cd00171
      Location:581 → 735
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:780 → 905
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:785 → 893
      PH; PH domain

    34. NM_206909.3 → NP_996792.1  PH and SEC7 domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_996792.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has distinct N- and C-termini compared to isoform a.
      Source sequence(s)
      AC120051, AF243495, AK091317, DB055312
      Consensus CDS
      CCDS34854.1
      UniProtKB/Swiss-Prot
      Q9NYI0
      UniProtKB/TrEMBL
      B3KRC4
      Related
      ENSP00000286485.8, ENST00000286485.12
      Conserved Domains (2) summary
      cd00171
      Location:47 → 201
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:246 → 371
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    RNA

    1. NR_182062.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC009884

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      18527303..19084805 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      18794850..19349609 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NYI0.2 GenPept UniProtKB/Swiss-Prot:Q9NYI0

    Gene LinkOut

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

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