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

Gene ID: 23362, updated on 9-Nov-2022

Summary

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

See PSD3 in Genome Data Viewer
Location:
8p22
Exon count:
29
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (18527303..19085012, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (18794850..19278517, 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 uncharacterized LOC124901896 Neighboring gene Sharpr-MPRA regulatory region 772 Neighboring gene ribosomal protein L35 pseudogene 6 Neighboring gene uncharacterized LOC124901897 Neighboring gene uncharacterized LOC124901895 Neighboring gene uncharacterized LOC107986868 Neighboring gene small nucleolar RNA SNORA62/SNORA6 family Neighboring gene uncharacterized LOC105379303 Neighboring gene uncharacterized LOC124901898 Neighboring gene uncharacterized LOC105379301 Neighboring gene uncharacterized LOC100128993 Neighboring gene ATPase plasma membrane Ca2+ transporting 1 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
 
involved_in regulation of catalytic activity 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
PubMed 
located_in ruffle membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

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

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC120051, AF243495, AK091317
    Related
    ENSP00000430640.1, ENST00000523619.5
    Conserved Domains (2) summary
    cd00171
    Location:548702
    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:747872
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
  2. NM_001412865.1NP_001399794.1  PH and SEC7 domain-containing protein 3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC100849, AC120051
  3. NM_001412866.1NP_001399795.1  PH and SEC7 domain-containing protein 3 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC100849, AC120051
  4. NM_001412867.1NP_001399796.1  PH and SEC7 domain-containing protein 3 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100849
  5. NM_001412868.1NP_001399797.1  PH and SEC7 domain-containing protein 3 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100849
  6. NM_001412869.1NP_001399798.1  PH and SEC7 domain-containing protein 3 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100849
  7. NM_001412870.1NP_001399799.1  PH and SEC7 domain-containing protein 3 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  8. NM_001412871.1NP_001399800.1  PH and SEC7 domain-containing protein 3 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  9. NM_001412872.1NP_001399801.1  PH and SEC7 domain-containing protein 3 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  10. NM_001412873.1NP_001399802.1  PH and SEC7 domain-containing protein 3 isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  11. NM_001412874.1NP_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_001412875.1NP_001399804.1  PH and SEC7 domain-containing protein 3 isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  13. NM_001412876.1NP_001399805.1  PH and SEC7 domain-containing protein 3 isoform 15

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800, AC120051
  14. NM_001412877.1NP_001399806.1  PH and SEC7 domain-containing protein 3 isoform 16

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420
  15. NM_001412879.1NP_001399808.1  PH and SEC7 domain-containing protein 3 isoform 17

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420
  16. NM_001412880.1NP_001399809.1  PH and SEC7 domain-containing protein 3 isoform 18

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420, AC100800
  17. NM_001412881.1NP_001399810.1  PH and SEC7 domain-containing protein 3 isoform 19

    Status: VALIDATED

    Source sequence(s)
    AC009884, AC087821, AC090420
  18. NM_001412882.1NP_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_001412883.1NP_001399812.1  PH and SEC7 domain-containing protein 3 isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
    UniProtKB/TrEMBL
    E5RJ29
  20. NM_001412884.1NP_001399813.1  PH and SEC7 domain-containing protein 3 isoform 20

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420
  21. NM_001412885.1NP_001399814.1  PH and SEC7 domain-containing protein 3 isoform 21

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
  22. NM_001412886.1NP_001399815.1  PH and SEC7 domain-containing protein 3 isoform 21

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
  23. NM_001412887.1NP_001399816.1  PH and SEC7 domain-containing protein 3 isoform 22

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420
  24. NM_001412888.1NP_001399817.1  PH and SEC7 domain-containing protein 3 isoform 21

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
  25. NM_001412889.1NP_001399818.1  PH and SEC7 domain-containing protein 3 isoform 21

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
  26. NM_001412890.1NP_001399819.1  PH and SEC7 domain-containing protein 3 isoform 23

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC090420, AC100800, AC120051
  27. NM_001412891.1NP_001399820.1  PH and SEC7 domain-containing protein 3 isoform 23

    Status: VALIDATED

    Source sequence(s)
    AC090420, AC100800, AC120051
  28. NM_001412892.1NP_001399821.1  PH and SEC7 domain-containing protein 3 isoform 25

    Status: VALIDATED

    Source sequence(s)
    AC090420
  29. NM_001412893.1NP_001399822.1  PH and SEC7 domain-containing protein 3 isoform 26

    Status: VALIDATED

    Source sequence(s)
    AC090420
  30. NM_001412894.1NP_001399823.1  PH and SEC7 domain-containing protein 3 isoform 27

    Status: VALIDATED

    Source sequence(s)
    AC090420
  31. NM_001412895.1NP_001399824.1  PH and SEC7 domain-containing protein 3 isoform 28

    Status: VALIDATED

    Source sequence(s)
    AC100800, AC120051
    UniProtKB/TrEMBL
    B4DKF8
  32. NM_001412896.1NP_001399825.1  PH and SEC7 domain-containing protein 3 isoform 29

    Status: VALIDATED

    Source sequence(s)
    AC100800, AC120051
  33. NM_015310.4NP_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
    Q9NYI0
    UniProtKB/TrEMBL
    B3KRC4
    Related
    ENSP00000324127.8, ENST00000327040.13
    Conserved Domains (3) summary
    cd00171
    Location:581735
    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:780905
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:785893
    PH; PH domain
  34. NM_206909.3NP_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:47201
    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:246371
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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..19085012 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421620.1XP_047277576.1  PH and SEC7 domain-containing protein 3 isoform X1

  2. XM_017013260.1XP_016868749.1  PH and SEC7 domain-containing protein 3 isoform X4

  3. XM_017013259.2XP_016868748.1  PH and SEC7 domain-containing protein 3 isoform X3

  4. XM_017013258.2XP_016868747.1  PH and SEC7 domain-containing protein 3 isoform X2

  5. XM_017013265.2XP_016868754.1  PH and SEC7 domain-containing protein 3 isoform X17

  6. XM_011544473.3XP_011542775.1  PH and SEC7 domain-containing protein 3 isoform X10

    Conserved Domains (1) summary
    cd00171
    Location:825969
    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 ...
  7. XM_011544467.3XP_011542769.1  PH and SEC7 domain-containing protein 3 isoform X6

    Conserved Domains (1) summary
    cd00171
    Location:825969
    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 ...
  8. XM_047421625.1XP_047277581.1  PH and SEC7 domain-containing protein 3 isoform X15

  9. XM_011544468.3XP_011542770.1  PH and SEC7 domain-containing protein 3 isoform X7

    Conserved Domains (1) summary
    cd00171
    Location:825970
    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 ...
  10. XM_017013262.2XP_016868751.1  PH and SEC7 domain-containing protein 3 isoform X5

  11. XM_047421622.1XP_047277578.1  PH and SEC7 domain-containing protein 3 isoform X12

  12. XM_011544469.3XP_011542771.1  PH and SEC7 domain-containing protein 3 isoform X8

    Conserved Domains (1) summary
    cd00171
    Location:825969
    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 ...
  13. XM_047421623.1XP_047277579.1  PH and SEC7 domain-containing protein 3 isoform X13

  14. XM_011544471.3XP_011542773.1  PH and SEC7 domain-containing protein 3 isoform X9

    Conserved Domains (1) summary
    cd00171
    Location:825972
    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 ...
  15. XM_047421624.1XP_047277580.1  PH and SEC7 domain-containing protein 3 isoform X14

  16. XM_017013263.2XP_016868752.1  PH and SEC7 domain-containing protein 3 isoform X11

  17. XM_017013264.2XP_016868753.1  PH and SEC7 domain-containing protein 3 isoform X16

RNA

  1. XR_007060727.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    18794850..19278517 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)