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

Gene ID: 23362, updated on 3-Apr-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 and regulation of catalytic activity. Predicted to be located in membrane. Predicted to be active in ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 17.3), adrenal (RPKM 6.3) and 19 other tissues See more
Orthologs
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Genomic context

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Location:
8p22
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (18527303..19084805, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (18794850..19349609, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (18384813..18871213, 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
  • 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 (38) 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_2023_10

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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