Aliases for FOCAD Gene

Aliases for FOCAD Gene

  • Focadhesin 2 3 4 5
  • KIAA1797 2 3 4
  • FLJ20375 2
  • FOCAD 5

External Ids for FOCAD Gene

Previous HGNC Symbols for FOCAD Gene

  • KIAA1797

Previous GeneCards Identifiers for FOCAD Gene

  • GC09P020659
  • GC09P020660
  • GC09P020663
  • GC09P020666

Summaries for FOCAD Gene

GeneCards Summary for FOCAD Gene

FOCAD (Focadhesin) is a Protein Coding gene. Diseases associated with FOCAD include Fraser Syndrome 1. Gene Ontology (GO) annotations related to this gene include binding.

UniProtKB/Swiss-Prot Summary for FOCAD Gene

Gene Wiki entry for FOCAD Gene

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

Genomics for FOCAD Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for FOCAD 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
GH09J020682 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 261.8 +26.3 26303 3.4 CHD2 TBP SP1 MXD4 MNT IKZF1 BRCA1 SMAD5 POLR2A ELF1 FOCAD MIR491 FOCAD-AS1 piR-45012-521 HACD4
GH09J020658 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +1.0 992 2.6 ZBTB10 NR2C1 CEBPB ZNF341 SIN3A KLF9 SMARCA5 ZNF2 ZFP37 FOXA1 FOCAD HSALNG0070330 piR-45012-521 piR-57176-644 FOCAD-AS1 HACD4
GH09J020619 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.6 -35.9 -35908 5.6 SP1 FEZF1 DEK CTCF ZIC2 THAP11 SIN3A ZNF511 ZNF639 TRIM22 MLLT3 KLHL9 FOCAD IFNA20P MIR491 HSALNG0070328 piR-39858-643 SLC24A2
GH09J020692 Enhancer 0.8 Ensembl 12.1 +34.6 34592 1.4 FEZF1 CEBPA HOMEZ KDM6A THAP11 FOXA2 ZNF511 MAFF SMAD4 SAP130 MIR491 FOCAD FOCAD-AS1 HACD4
GH09J020941 Enhancer 0.9 Ensembl ENCODE 10.8 +282.9 282930 0.5 CTCF TRIM22 SMC3 RAD21 RFX5 YY1 SMARCA5 THRB ZNF2 ZFP37 HACD4 MLLT3 FOCAD HSALNG0070336 MN309174-651
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FOCAD on the GeneHancer Hub at the UCSC Golden Path

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

Genomic Locations for FOCAD Gene

Latest Assembly
chr9:20,658,309-20,995,955
(GRCh38/hg38)
Size:
337,647 bases
Orientation:
Plus strand

Previous Assembly
chr9:20,658,308-20,995,949
(GRCh37/hg19 by Entrez Gene)
Size:
337,642 bases
Orientation:
Plus strand

chr9:20,658,308-20,995,954
(GRCh37/hg19 by Ensembl)
Size:
337,647 bases
Orientation:
Plus strand

Genomic View for FOCAD Gene

Genes around FOCAD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for FOCAD Gene

Proteins for FOCAD Gene

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

    Protein Symbol:
    Q5VW36-FOCAD_HUMAN
    Recommended name:
    Focadhesin
    Protein Accession:
    Q5VW36
    Secondary Accessions:
    • D3DRJ9
    • Q6ZME1
    • Q8IZG0
    • Q96JM8
    • Q96MS9
    • Q9BVF3
    • Q9NX87

    Protein attributes for FOCAD Gene

    Size:
    1801 amino acids
    Molecular mass:
    200072 Da
    Quaternary structure:
    • Interacts with VCL.
    SequenceCaution:
    • Sequence=BAA91129.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91129.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAD18787.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for FOCAD Gene

Post-translational modifications for FOCAD Gene

  • Ubiquitination at Lys553, Lys577, Lys583, Lys799, and Lys1777
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for FOCAD Gene

Domains & Families for FOCAD Gene

Gene Families for FOCAD Gene

Protein Domains for FOCAD Gene

InterPro:
Blocks:
  • HEAT repeat
ProtoNet:
genes like me logo Genes that share domains with FOCAD: view

No data available for Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for FOCAD Gene

Function for FOCAD Gene

Molecular function for FOCAD Gene

UniProtKB/Swiss-Prot Function:
Potential tumor suppressor in gliomas.

Phenotypes From GWAS Catalog for FOCAD Gene

Gene Ontology (GO) - Molecular Function for FOCAD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22427331
genes like me logo Genes that share ontologies with FOCAD: view
genes like me logo Genes that share phenotypes with FOCAD: view

Inhibitory RNAs for research

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

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

Localization for FOCAD Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOCAD Gene

Membrane. Multi-pass membrane protein. Cell junction, focal adhesion. Note=Colocalizes with VCL in astrocytes.

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 FOCAD gene
Compartment Confidence
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for FOCAD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005925 focal adhesion IEA,IDA 22427331
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with FOCAD: view

Pathways & Interactions for FOCAD Gene

PathCards logo

SuperPathways for FOCAD Gene

No Data Available

Gene Ontology (GO) - Biological Process for FOCAD Gene

None

No data available for Pathways by source and SIGNOR curated interactions for FOCAD Gene

Drugs & Compounds for FOCAD Gene

No Compound Related Data Available

Transcripts for FOCAD Gene

mRNA/cDNA for FOCAD Gene

4 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
SP1:
SP2: -
SP3: - -
SP4: - -
SP5:

Relevant External Links for FOCAD Gene

GeneLoc Exon Structure for
FOCAD

Expression for FOCAD Gene

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

Protein differential expression in normal tissues from HIPED for FOCAD Gene

This gene is overexpressed in Stomach (16.3), Adrenal (8.7), Plasma (7.3), and Lymph node (6.9).

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



Protein tissue co-expression partners for FOCAD Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for FOCAD Gene:

Hs.136247

mRNA Expression by UniProt/SwissProt for FOCAD Gene:

Q5VW36-FOCAD_HUMAN
Tissue specificity: Ubiquitous. High expression in brain followed by testis, muscle, pancreas, heart, ovary, small intestine, placenta, prostate, thymus, kidney, colon, liver, lung, spleen and leukocytes. Expression is reduced in most glioblastomas and all glioblastoma cell lines.

Evidence on tissue expression from TISSUES for FOCAD Gene

  • Nervous system(4.8)
  • Heart(4.3)
genes like me logo Genes that share expression patterns with FOCAD: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for FOCAD Gene

Orthologs for FOCAD Gene

This gene was present in the common ancestor of animals.

Orthologs for FOCAD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia FOCAD 30 31
  • 99.48 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia FOCAD 30
  • 89.25 (n)
KIAA1797 31
  • 89 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia FOCAD 30 31
  • 88.77 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Focad 30 17 31
  • 84.63 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Focad 30
  • 84.59 (n)
Oppossum
(Monodelphis domestica)
Mammalia FOCAD 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 75 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
-- 31
  • 68 (a)
OneToMany
-- 31
  • 67 (a)
OneToMany
Chicken
(Gallus gallus)
Aves FOCAD 30 31
  • 70.19 (n)
OneToMany
-- 31
  • 56 (a)
OneToMany
-- 31
  • 52 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia FOCAD 31
  • 67 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii focad 30
  • 56.71 (n)
FOCAD 31
  • 50 (a)
OneToOne
Dr.16271 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG3520 31
  • 21 (a)
OneToOne
Species where no ortholog for FOCAD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 Vase (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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for FOCAD Gene

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

Paralogs for FOCAD Gene

No data available for Paralogs for FOCAD Gene

Variants for FOCAD Gene

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

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs1019593703 Likely Benign: not provided 20,990,116(+) A/G
NM_017794.4(FOCAD):c.5005-7A>G
INTRON
rs10441706 Benign: not provided. - 20,770,032(+) G/Ap.Val234Ile
NM_017794.4(FOCAD):c.700G>A (p.Val234Ile)
MISSENSE
rs10511687 Benign: not specified. - 20,764,871(+) T/Cp.Leu166Ser
NM_017794.4(FOCAD):c.497T>C (p.Leu166Ser)
MISSENSE
rs111967925 Benign: not provided 20,933,020(+) A/C
NM_017794.4(FOCAD):c.3324A>C (p.Ile1108=)
SYNONYMOUS
rs116541636 Likely Benign: not provided 20,976,422(+) C/T
NM_017794.4(FOCAD):c.4135C>T (p.Pro1379Ser)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FOCAD Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv1761789 CNV deletion 17803354
esv1962655 CNV deletion 18987734
esv2421522 CNV deletion 20811451
esv2659270 CNV deletion 23128226
esv2738270 CNV deletion 23290073
esv2738271 CNV deletion 23290073
esv2759677 CNV loss 17122850
esv2764150 CNV gain+loss 21179565
esv3451468 CNV insertion 20981092
esv3576641 CNV gain 25503493
esv3619939 CNV loss 21293372
esv3619940 CNV loss 21293372
esv3619941 CNV loss 21293372
esv3619943 CNV loss 21293372
esv3619944 CNV gain 21293372
esv3619945 CNV loss 21293372
esv3891632 CNV gain 25118596
nsv1015492 CNV loss 25217958
nsv1017312 CNV gain 25217958
nsv1024327 CNV loss 25217958
nsv1028928 CNV loss 25217958
nsv1032837 CNV loss 25217958
nsv1161846 CNV deletion 26073780
nsv437645 CNV loss 16327808
nsv442137 CNV loss 18776908
nsv466291 CNV loss 19166990
nsv466292 CNV gain 19166990
nsv507509 OTHER sequence alteration 20534489
nsv510188 OTHER sequence alteration 20534489
nsv516765 CNV loss 19592680
nsv518943 CNV loss 19592680
nsv523258 CNV loss 19592680
nsv524000 CNV loss 19592680
nsv524984 CNV loss 19592680
nsv527232 CNV loss 19592680
nsv613747 CNV loss 21841781
nsv613748 CNV loss 21841781
nsv613749 CNV loss 21841781
nsv613750 CNV gain 21841781
nsv613751 CNV loss 21841781
nsv6499 CNV insertion 18451855
nsv824873 CNV loss 20364138
nsv824874 CNV loss 20364138

Variation tolerance for FOCAD Gene

Residual Variation Intolerance Score: 70.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.10; 97.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOCAD Gene

Human Gene Mutation Database (HGMD)
FOCAD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOCAD

SNP Genotyping and Copy Number Assays for research

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

Disorders for FOCAD Gene

MalaCards: The human disease database

(1) MalaCards diseases for FOCAD Gene - From: COP

Disorder Aliases PubMed IDs
fraser syndrome 1
  • frasrs1
- elite association - COSMIC cancer census association via MalaCards
Search FOCAD in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FOCAD

genes like me logo Genes that share disorders with FOCAD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FOCAD Gene

Publications for FOCAD Gene

  1. KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas. (PMID: 22427331) Brockschmidt A … Weber RG (Brain : a journal of neurology 2012) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4
  4. FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas. (PMID: 31473790) Brand F … Weber RG (Acta neuropathologica 2020) 3
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3

Products for FOCAD Gene

Sources for FOCAD Gene