CACHD1 Gene (Protein Coding)

Cache Domain Containing 1

GC01P064470
GIFtS:
35
See more...

Aliases for CACHD1 Gene

Aliases for CACHD1 Gene

  • Cache Domain Containing 1 2 3 5
  • Von Willebrand Factor Type A And Cache Domain Containing 1 2 3
  • VWFA And Cache Domain-Containing Protein 1 3 4
  • Cache Domain-Containing Protein 1 3 4
  • KIAA1573 2 4
  • CACHD1 5
  • VWCD1 4

External Ids for CACHD1 Gene

Previous HGNC Symbols for CACHD1 Gene

  • VWCD1

Previous GeneCards Identifiers for CACHD1 Gene

  • GC01P064685
  • GC01P064936
  • GC01P063045

Summaries for CACHD1 Gene

GeneCards Summary for CACHD1 Gene

CACHD1 (Cache Domain Containing 1) is a Protein Coding gene. Diseases associated with CACHD1 include Cercarial Dermatitis and Hypertropia. An important paralog of this gene is CACNA2D3.

UniProtKB/Swiss-Prot Summary for CACHD1 Gene

Additional gene information for CACHD1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CACHD1 Gene

Genomics for CACHD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CACHD1 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
GH01J064470 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 257.8 +3.2 3226 8.3 ZSCAN16 ZBTB10 FEZF1 CTCF ZIC2 ZNF610 ZNF513 SIN3A GABPA KLF7 CACHD1 ITGB3BP 5MWI_A-003 HSALNG0004159 LOC107984966 RAVER2
GH01J064505 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 262.4 +35.7 35698 2.1 FEZF1 ZEB1 ELF1 ZNF513 ZNF639 VEZF1 KLF7 ZNF341 SIN3A ZNF843 CACHD1 ITGB3BP LINC01359 HSALNG0004160 5MWI_A-003 RAVER2
GH01J064493 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 22.6 +25.9 25872 7.2 FEZF1 MAFF YY1 ZNF316 PRDM6 MAFK HNF4A MAFG POU5F1 NANOG CACHD1 RAVER2 5MWI_A-003 HSALNG0004160
GH01J064522 Enhancer 0.9 Ensembl CraniofacialAtlas dbSUPER 22.6 +55.2 55172 6.2 ZNF513 ZNF316 REST SCRT1 ZNF530 MAFK NANOG USF1 ZNF600 CACHD1 HSALNG0004160 MIR4794 RAVER2
GH01J064536 Enhancer 1 ENCODE CraniofacialAtlas dbSUPER 10.7 +67.0 67023 0.9 FEZF1 RXRA FOXA2 ZBTB33 JUND KLF16 HNF4A FOXA1 RAD21 REST CACHD1 HSALNG0004160 MIR4794 RAVER2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CACHD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CACHD1

Top Transcription factor binding sites by QIAGEN in the CACHD1 gene promoter:
  • C/EBPalpha
  • GATA-2
  • MZF-1
  • NF-1
  • Nkx2-5
  • Pax-2
  • Pax-2a
  • S8

Genomic Locations for CACHD1 Gene

Latest Assembly
chr1:64,470,129-64,693,058
(GRCh38/hg38)
Size:
222,930 bases
Orientation:
Plus strand

Previous Assembly
chr1:64,935,812-65,158,736
(GRCh37/hg19 by Entrez Gene)
Size:
222,925 bases
Orientation:
Plus strand

chr1:64,936,428-65,158,741
(GRCh37/hg19 by Ensembl)
Size:
222,314 bases
Orientation:
Plus strand

Genomic View for CACHD1 Gene

Genes around CACHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CACHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CACHD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CACHD1 Gene

Proteins for CACHD1 Gene

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  3. Assay products for research

  • Protein details for CACHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VU97-CAHD1_HUMAN
    Recommended name:
    VWFA and cache domain-containing protein 1
    Protein Accession:
    Q5VU97
    Secondary Accessions:
    • Q49AE9
    • Q658T4
    • Q7Z3P2
    • Q9H7W4
    • Q9H9W3
    • Q9HCJ9

    Protein attributes for CACHD1 Gene

    Size:
    1274 amino acids
    Molecular mass:
    142290 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB14105.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14860.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CACHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CACHD1 Gene

Protein Expression for CACHD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CACHD1 Gene

  • Glycosylation at Asn145 and Asn587
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CAHD1_HUMAN (1901)

Other Protein References for CACHD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CACHD1 Gene

Domains & Families for CACHD1 Gene

Gene Families for CACHD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for CACHD1 Gene

InterPro:
Blocks:
  • Cache domain
ProtoNet:

Suggested Antigen Peptide Sequences for CACHD1 Gene

GenScript: Design optimal peptide antigens:
  • VWFA and cache domain-containing protein 1 (CAHD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5VU97

UniProtKB/Swiss-Prot:

CAHD1_HUMAN :
  • Belongs to the calcium channel subunit alpha-2/delta family.
Family:
  • Belongs to the calcium channel subunit alpha-2/delta family.
genes like me logo Genes that share domains with CACHD1: view

Function for CACHD1 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for CACHD1 Gene

UniProtKB/Swiss-Prot Function:
May regulate voltage-dependent calcium channels.

Phenotypes From GWAS Catalog for CACHD1 Gene

Gene Ontology (GO) - Molecular Function for CACHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005245 voltage-gated calcium channel activity IBA 21873635
genes like me logo Genes that share ontologies with CACHD1: view

Phenotypes for CACHD1 Gene

MGI mutant phenotypes for CACHD1:
inferred from 1 alleles
GenomeRNAi human phenotypes for CACHD1:
genes like me logo Genes that share phenotypes with CACHD1: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CACHD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CACHD1 Gene

Localization for CACHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CACHD1 Gene

Membrane. Single-pass type I membrane protein.

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 CACHD1 gene
Compartment Confidence
plasma membrane 3
nucleus 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CACHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005891 voltage-gated calcium channel complex IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CACHD1: view

Pathways & Interactions for CACHD1 Gene

PathCards logo

SuperPathways for CACHD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CACHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006816 calcium ion transport IEA --
GO:0070588 calcium ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with CACHD1: view

No data available for Pathways by source and SIGNOR curated interactions for CACHD1 Gene

Drugs & Compounds for CACHD1 Gene

Products:

  1. Drug products for research

(1) Drugs for CACHD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876
genes like me logo Genes that share compounds with CACHD1: view

Transcripts for CACHD1 Gene

Products:

  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for CACHD1 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
6 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 CACHD1

Alternative Splicing Database (ASD) splice patterns (SP) for CACHD1 Gene

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

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for CACHD1 Gene

GeneLoc Exon Structure for
CACHD1

Expression for CACHD1 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CACHD1 Gene

mRNA expression in normal human tissues for CACHD1 Gene
mRNA expression by BioGPS for CACHD1 GenemRNA expression by GTEx for CACHD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CACHD1 Gene

This gene is overexpressed in CD4 Tcells (23.7) and Liver (23.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CACHD1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CACHD1

SOURCE GeneReport for Unigene cluster for CACHD1 Gene:

Hs.443891

Evidence on tissue expression from TISSUES for CACHD1 Gene

  • Nervous system(4.5)
  • Stomach(4.1)
genes like me logo Genes that share expression patterns with CACHD1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CACHD1 Gene

Orthologs for CACHD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CACHD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CACHD1 30 31
  • 99.67 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CACHD1 30 31
  • 92.62 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CACHD1 30 31
  • 92.45 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CACHD1 31
  • 90 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 90 (a)
 OneToMany
-- 31
  • 77 (a)
 OneToMany
Rat
(Rattus norvegicus)
 Mammalia Cachd1 30
  • 89.92 (n)
Mouse
(Mus musculus)
 Mammalia Cachd1 30 17 31
  • 89.62 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves CACHD1 30 31
  • 82.61 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CACHD1 31
  • 90 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia cachd1 30
  • 78.39 (n)
Str.2042 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.10935 30
Zebrafish
(Danio rerio)
 Actinopterygii cachd1 30 31
  • 75.99 (n)
 OneToOne
Dr.15338 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP009043 30
  • 48.7 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG16868 30 31
  • 47.14 (n)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 43 (a)
 OneToMany
-- 31
  • 41 (a)
 OneToMany
-- 31
  • 30 (a)
 OneToMany
-- 31
  • 29 (a)
 OneToMany
-- 31
  • 24 (a)
 OneToMany
Species where no ortholog for CACHD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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)
  • Worm (Caenorhabditis elegans)

Evolution for CACHD1 Gene

ENSEMBL:
Gene Tree for CACHD1 (if available)
TreeFam:
Gene Tree for CACHD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CACHD1: view image

Paralogs for CACHD1 Gene

Paralogs for CACHD1 Gene

genes like me logo Genes that share paralogs with CACHD1: view

Variants for CACHD1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CACHD1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
973047 Not Provided: not provided 64,648,031(+) G/A
NM_020925.4(CACHD1):c.1387G>A (p.Asp463Asn) 		MISSENSE
rs201614737 Not Provided: not provided 64,582,187(+) G/A
NM_020925.4(CACHD1):c.293G>A (p.Arg98His) 		MISSENSE_VARIANT,FIVE_PRIME_UTR
rs750499224 Not Provided: not provided 64,678,313(+) A/G
NM_020925.4(CACHD1):c.3244+3A>G 		INTRON
rs6588100 - p.Met414Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CACHD1 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 CACHD1 Gene

Variant ID Type Subtype PubMed ID
esv1280177 CNV insertion 17803354
esv1980143 CNV deletion 18987734
esv2660804 CNV deletion 23128226
esv2667664 CNV deletion 23128226
esv2749152 CNV deletion 23290073
esv3303888 CNV mobile element insertion 20981092
esv3309582 CNV mobile element insertion 20981092
esv3410076 CNV insertion 20981092
esv3586265 CNV loss 21293372
esv3586268 CNV loss 21293372
esv3586269 CNV loss 21293372
nsv1000188 CNV gain 25217958
nsv1077372 CNV deletion 25765185
nsv1119693 CNV deletion 24896259
nsv1122355 CNV deletion 24896259
nsv1136083 CNV deletion 24896259
nsv1139480 CNV duplication 24896259
nsv1153414 CNV deletion 26484159
nsv471992 CNV novel sequence insertion 20440878
nsv508237 CNV deletion 20534489
nsv522029 CNV loss 19592680
nsv546437 CNV loss 21841781
nsv830048 CNV gain 17160897

Variation tolerance for CACHD1 Gene

Residual Variation Intolerance Score: 27.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.48; 71.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CACHD1 Gene

Human Gene Mutation Database (HGMD)
CACHD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CACHD1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CACHD1 Gene

Disorders for CACHD1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CACHD1 Gene - From: COP

Disorder Aliases PubMed IDs
cercarial dermatitis
  • cutaneous schistosomiasis
hypertropia
46,xy sex reversal 8
  • srxy8
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CACHD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CACHD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CACHD1 Gene

Publications for CACHD1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
  2. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling. (PMID: 31073040) Choi JH … Beutler B (Science (New York, N.Y.) 2019) 3
  5. CACHD1: A new activity-modifying protein for voltage-gated calcium channels. (PMID: 30983497) Stephens GJ … Cottrell GS (Channels (Austin, Tex.) 2019) 3

ExternalLinks

View latest publications for CACHD1 gene in Mastermind

Products for CACHD1 Gene

Sources for CACHD1 Gene