Aliases for VEPH1 Gene

Aliases for VEPH1 Gene

  • Ventricular Zone Expressed PH Domain Containing 1 2 3 5
  • Ventricular Zone-Expressed PH Domain-Containing Protein Homolog 1 3 4
  • Protein Melted 3 4
  • VEPH 3 4
  • Ventricular Zone Expressed PH Domain Homolog 1 (Zebrafish) 2
  • Ventricular Zone Expressed PH Domain Homolog 1 3
  • KIAA1692 4
  • MELT 3

External Ids for VEPH1 Gene

Previous GeneCards Identifiers for VEPH1 Gene

  • GC03M158461
  • GC03M156977
  • GC03M154373

Summaries for VEPH1 Gene

GeneCards Summary for VEPH1 Gene

VEPH1 (Ventricular Zone Expressed PH Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include binding.

UniProtKB/Swiss-Prot Summary for VEPH1 Gene

  • Interacts with TGF-beta receptor type-1 (TGFBR1) and inhibits dissociation of activated SMAD2 from TGFBR1, impeding its nuclear accumulation and resulting in impaired TGF-beta signaling. May also affect FOXO, Hippo and Wnt signaling.

Additional gene information for VEPH1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VEPH1 Gene

Genomics for VEPH1 Gene

GeneHancer (GH) Regulatory Elements for VEPH1 Gene

Promoters and enhancers for VEPH1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J157530 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 519.6 +1.3 1339 4.3 ZNF217 CTCF FOS ZBTB11 REST RAD21 TRIM22 SMC3 NFRKB ZNF316 VEPH1 SLC66A1L lnc-CCNL1-8
GH03J157502 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE CraniofacialAtlas 517.2 +30.1 30050 2.3 NR3C1 PBX2 JUND GATA3 PKNOX1 ESR1 GATA2 VEPH1 SLC66A1L lnc-CCNL1-8
GH03J157534 Enhancer 0.9 ENCODE dbSUPER 500.7 -1.2 -1231 0.4 CTCF CTBP1 NCOR1 ZNF316 ARNT TRIM24 NFE2 FOSL1 TAL1 FOS VEPH1 SLC66A1L
GH03J157542 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE CraniofacialAtlas 16.6 -9.7 -9682 1.4 CTCF HDAC2 MXI1 MYC YY1 USF1 POLR2A RAD21 CTBP2 ZNF143 SLC66A1L NONHSAG036498.2 VEPH1
GH03J157526 Enhancer 0.8 ENCODE dbSUPER 17.6 +5.5 5516 2.4 NCOR1 PBX2 USF1 TAL1 MAFK ZBTB40 FOXP2 MITF TOE1 USF2 VEPH1 SLC66A1L lnc-CCNL1-8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VEPH1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VEPH1

Top Transcription factor binding sites by QIAGEN in the VEPH1 gene promoter:
  • LHX3b
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for VEPH1 Gene

Genomic Locations for VEPH1 Gene
chr3:157,259,742-157,533,619
(GRCh38/hg38)
Size:
273,878 bases
Orientation:
Minus strand
chr3:156,977,531-157,251,408
(GRCh37/hg19)
Size:
273,878 bases
Orientation:
Minus strand

Genomic View for VEPH1 Gene

Genes around VEPH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VEPH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VEPH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VEPH1 Gene

Proteins for VEPH1 Gene

  • Protein details for VEPH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14D04-MELT_HUMAN
    Recommended name:
    Ventricular zone-expressed PH domain-containing protein homolog 1
    Protein Accession:
    Q14D04
    Secondary Accessions:
    • D3DNL0
    • F5GZ91
    • Q2TAA9
    • Q3MIX2
    • Q6PEL3
    • Q86TL5
    • Q8TCR3
    • Q96SP7
    • Q9C0H1
    • Q9H9Q7

    Protein attributes for VEPH1 Gene

    Size:
    833 amino acids
    Molecular mass:
    94745 Da
    Quaternary structure:
    • Interacts with TGFBR1.
    SequenceCaution:
    • Sequence=BAB14165.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB21783.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VEPH1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VEPH1 Gene

Post-translational modifications for VEPH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VEPH1 Gene

Domains & Families for VEPH1 Gene

Gene Families for VEPH1 Gene

Protein Domains for VEPH1 Gene

Suggested Antigen Peptide Sequences for VEPH1 Gene

GenScript: Design optimal peptide antigens:
  • Protein melted (MELT_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q14D04

UniProtKB/Swiss-Prot:

MELT_HUMAN :
  • The PH domain is required for membrane targeting.
  • Belongs to the MELT/VEPH family.
Domain:
  • The PH domain is required for membrane targeting.
Family:
  • Belongs to the MELT/VEPH family.
genes like me logo Genes that share domains with VEPH1: view

Function for VEPH1 Gene

Molecular function for VEPH1 Gene

UniProtKB/Swiss-Prot Function:
Interacts with TGF-beta receptor type-1 (TGFBR1) and inhibits dissociation of activated SMAD2 from TGFBR1, impeding its nuclear accumulation and resulting in impaired TGF-beta signaling. May also affect FOXO, Hippo and Wnt signaling.

Phenotypes From GWAS Catalog for VEPH1 Gene

Gene Ontology (GO) - Molecular Function for VEPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 30126976
genes like me logo Genes that share ontologies with VEPH1: view
genes like me logo Genes that share phenotypes with VEPH1: view

Animal Models for VEPH1 Gene

MGI Knock Outs for VEPH1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VEPH1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VEPH1 Gene

Localization for VEPH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VEPH1 Gene

Cell membrane; Peripheral membrane protein; Cytoplasmic side.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VEPH1 gene
Compartment Confidence
plasma membrane 3
nucleus 3
cytosol 3
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VEPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with VEPH1: view

Pathways & Interactions for VEPH1 Gene

PathCards logo

SuperPathways for VEPH1 Gene

No Data Available

Interacting Proteins for VEPH1 Gene

;

SIGNOR curated interactions for VEPH1 Gene

Activates:
Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for VEPH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway IDA 26039994
GO:0060392 negative regulation of SMAD protein signal transduction IDA 26039994
genes like me logo Genes that share ontologies with VEPH1: view

No data available for Pathways by source for VEPH1 Gene

Drugs & Compounds for VEPH1 Gene

No Compound Related Data Available

Transcripts for VEPH1 Gene

mRNA/cDNA for VEPH1 Gene

6 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
19 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VEPH1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VEPH1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18
SP1: - - - - -
SP2: - - -
SP3: - - -
SP4: - - - - -
SP5:
SP6:
SP7: -

Relevant External Links for VEPH1 Gene

GeneLoc Exon Structure for
VEPH1

Expression for VEPH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VEPH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VEPH1 Gene

This gene is overexpressed in Adrenal Gland (x10.5), Pituitary (x10.3), Lung (x8.0), and Kidney - Cortex (x4.5).

Protein differential expression in normal tissues from HIPED for VEPH1 Gene

This gene is overexpressed in Cervix (58.6) and Heart (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VEPH1 Gene



Protein tissue co-expression partners for VEPH1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VEPH1

SOURCE GeneReport for Unigene cluster for VEPH1 Gene:

Hs.658046

Evidence on tissue expression from TISSUES for VEPH1 Gene

  • Kidney(4.3)
  • Skin(4.1)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with VEPH1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VEPH1 Gene

Orthologs for VEPH1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VEPH1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VEPH1 31 30
  • 99.56 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 86 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
-- 31
  • 66 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
cow
(Bos Taurus)
Mammalia VEPH1 31 30
  • 90.28 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VEPH1 31 30
  • 87.43 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Veph1 17 31 30
  • 85.15 (n)
rat
(Rattus norvegicus)
Mammalia Veph1 30
  • 84.25 (n)
oppossum
(Monodelphis domestica)
Mammalia VEPH1 31
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves VEPH1 31 30
  • 73.56 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VEPH1 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia veph1 30
  • 66.99 (n)
zebrafish
(Danio rerio)
Actinopterygii veph 31 30
  • 62.63 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta melt 31 30
  • 48.29 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007472 30
  • 48.1 (n)
worm
(Caenorhabditis elegans)
Secernentea K10B4.3 31 30
  • 45.33 (n)
OneToOne
Species where no ortholog for VEPH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VEPH1 Gene

ENSEMBL:
Gene Tree for VEPH1 (if available)
TreeFam:
Gene Tree for VEPH1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VEPH1: view image

Paralogs for VEPH1 Gene

No data available for Paralogs for VEPH1 Gene

Variants for VEPH1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VEPH1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
714212 Benign: not provided 157,442,628(-) A/T SYNONYMOUS_VARIANT,INTRON_VARIANT
731088 Benign: not provided 157,442,912(-) G/A MISSENSE_VARIANT,INTRON_VARIANT
770537 Benign: not provided 157,436,979(-) T/C SYNONYMOUS_VARIANT,INTRON_VARIANT
770895 Benign: not provided 157,437,882(-) A/G MISSENSE_VARIANT,INTRON_VARIANT
784028 Benign: not provided 157,437,050(-) T/G MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for VEPH1 Gene

Structural Variations from Database of Genomic Variants (DGV) for VEPH1 Gene

Variant ID Type Subtype PubMed ID
esv2582112 CNV deletion 19546169
esv275099 CNV gain+loss 21479260
esv2759193 CNV gain 17122850
esv32988 CNV loss 17666407
esv3306702 CNV mobile element insertion 20981092
esv3309768 CNV mobile element insertion 20981092
esv3324631 CNV insertion 20981092
esv3360628 CNV insertion 20981092
esv3431834 CNV insertion 20981092
nsv236425 CNV insertion 16902084
nsv829766 CNV gain 17160897

Variation tolerance for VEPH1 Gene

Residual Variation Intolerance Score: 92.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.74; 93.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VEPH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VEPH1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VEPH1 Gene

Disorders for VEPH1 Gene

Additional Disease Information for VEPH1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for VEPH1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VEPH1 Gene

Publications for VEPH1 Gene

  1. Identification and characterization of Veph, a novel gene encoding a PH domain-containing protein expressed in the developing central nervous system of vertebrates. (PMID: 15388229) Muto E … Watanabe S (Biochimie 2004) 2 3 4 54
  2. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 54
  3. Human ortholog of Drosophila Melted impedes SMAD2 release from TGF-β receptor I to inhibit TGF-β signaling. (PMID: 26039994) Shathasivam P … Brown TJ (Proceedings of the National Academy of Sciences of the United States of America 2015) 3 4 54
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41 54

Products for VEPH1 Gene

Sources for VEPH1 Gene