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Aliases for HMCN1 Gene

Aliases for HMCN1 Gene

  • Hemicentin 1 2 3 5
  • Fibulin-6 3 4
  • FIBL-6 3 4
  • FIBL6 3 4
  • Age-Related Macular Degeneration 1 (Senile Macular Degeneration) 2
  • Hemicentin-1 3
  • EC 2.7.10.1 61
  • EC 3.6.5.5 61
  • Fibulin 6 2
  • FBLN6 3
  • ARMD1 3

External Ids for HMCN1 Gene

Previous HGNC Symbols for HMCN1 Gene

  • ARMD1

Previous GeneCards Identifiers for HMCN1 Gene

  • GC01P182436
  • GC01P183970
  • GC01P156939

Summaries for HMCN1 Gene

Entrez Gene Summary for HMCN1 Gene

  • This gene encodes a large extracellular member of the immunoglobulin superfamily. A similar protein in C. elegans forms long, fine tracks at specific extracellular sites that are involved in many processes such as stabilization of the germline syncytium, anchorage of mechanosensory neurons to the epidermis, and organization of hemidesmosomes in the epidermis. Mutations in this gene may be associated with age-related macular degeneration. [provided by RefSeq, Jul 2008]

GeneCards Summary for HMCN1 Gene

HMCN1 (Hemicentin 1) is a Protein Coding gene. Diseases associated with HMCN1 include Macular Degeneration, Age-Related, 1 and Postpartum Depression. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is HMCN2.

UniProtKB/Swiss-Prot for HMCN1 Gene

  • Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration.

Gene Wiki entry for HMCN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMCN1 Gene

Genomics for HMCN1 Gene

Regulatory Elements for HMCN1 Gene

Enhancers for HMCN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G185693 1.1 Ensembl ENCODE 18 -40.1 -40148 1.3 BRD4 FOXA2 CBX3 MAX RAD21 ZBTB40 RELA YY1 TEAD3 POLR2A HMCN1 GS1-204I12.4
GH01G186081 1.6 FANTOM5 Ensembl ENCODE 9.2 +348.4 348387 2.0 PKNOX1 FOXA2 ARNT FEZF1 ZNF766 CBX5 ZNF263 SP3 JUNB REST HMCN1 PDC ENSG00000224691 GC01M185927
GH01G185695 0.5 ENCODE 17.9 -38.9 -38898 0.1 CTCF ZNF654 GATA3 SMC3 RAD21 HMCN1 GS1-204I12.4
GH01G186073 0.4 FANTOM5 20.4 +339.6 339625 0.4 MTA2 HMCN1 OCLM ENSG00000224691 GC01M185927
GH01G185718 0.9 Ensembl ENCODE 7.3 -15.0 -14992 1.9 ZNF263 CTCF RAD21 YY1 ATF3 SMC3 PCBP1 FOS HNF4A HMCN1 GS1-204I12.4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMCN1 on UCSC Golden Path with GeneCards custom track

Promoters for HMCN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000017165 420 2399 FOXA2 DMAP1 ZNF2 GLIS2 ZNF302 GATA2 ZNF263 SP3 NFYC ZNF579

Genomic Location for HMCN1 Gene

Chromosome:
1
Start:
185,734,381 bp from pter
End:
186,190,953 bp from pter
Size:
456,573 bases
Orientation:
Plus strand

Genomic View for HMCN1 Gene

Genes around HMCN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMCN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMCN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMCN1 Gene

Proteins for HMCN1 Gene

  • Protein details for HMCN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96RW7-HMCN1_HUMAN
    Recommended name:
    Hemicentin-1
    Protein Accession:
    Q96RW7
    Secondary Accessions:
    • A6NGE3
    • Q5TYR7
    • Q96DN3
    • Q96DN8
    • Q96SC3

    Protein attributes for HMCN1 Gene

    Size:
    5635 amino acids
    Molecular mass:
    613390 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB71154.1; Type=Frameshift; Positions=657; Evidence={ECO:0000305}; Sequence=BAB71216.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for HMCN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HMCN1 Gene

Selected DME Specific Peptides for HMCN1 Gene

Q96RW7:
  • YSCVASN
  • SLSWYKD

Post-translational modifications for HMCN1 Gene

  • Glycosylation at isoforms=2349, posLast=390390, isoforms=2528, isoforms=2550, posLast=573573, isoforms=2, 3620, isoforms=2, 3693, posLast=809809, posLast=970970, posLast=11581158, posLast=12721272, isoforms=21369, posLast=15521552, posLast=19291929, isoforms=22112, posLast=21552155, posLast=23952395, posLast=26892689, posLast=28872887, posLast=29732973, posLast=32213221, isoforms=23300, posLast=35303530, isoforms=23689, posLast=37273727, posLast=38123812, posLast=40294029, isoforms=24401, posLast=44914491, posLast=46064606, posLast=48944894, posLast=50405040, posLast=52675267, and posLast=56155615
  • Modification sites at PhosphoSitePlus

Other Protein References for HMCN1 Gene

Domains & Families for HMCN1 Gene

No data available for UniProtKB/Swiss-Prot for HMCN1 Gene

Function for HMCN1 Gene

Molecular function for HMCN1 Gene

UniProtKB/Swiss-Prot Function:
Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration.

Enzyme Numbers (IUBMB) for HMCN1 Gene

Gene Ontology (GO) - Molecular Function for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with HMCN1: view

Phenotypes for HMCN1 Gene

GenomeRNAi human phenotypes for HMCN1:
genes like me logo Genes that share phenotypes with HMCN1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HMCN1

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMCN1 Gene

Localization for HMCN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMCN1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane. Cytoplasm. Cell junction. Cleavage furrow. Note=The antibody used to determine subcellular location does not distinguish between HMCN1 and HMCN2. {ECO:0000250 UniProtKB:D3YXG0}.

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 HMCN1 gene
Compartment Confidence
extracellular 5
plasma membrane 3
nucleus 2
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005604 basement membrane IEA --
GO:0005737 cytoplasm IEA --
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with HMCN1: view

Pathways & Interactions for HMCN1 Gene

SuperPathways for HMCN1 Gene

No Data Available

Interacting Proteins for HMCN1 Gene

Gene Ontology (GO) - Biological Process for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007601 visual perception IEA --
GO:0050896 response to stimulus IEA --
GO:0051301 cell division IEA --
genes like me logo Genes that share ontologies with HMCN1: view

No data available for Pathways by source and SIGNOR curated interactions for HMCN1 Gene

Drugs & Compounds for HMCN1 Gene

No Compound Related Data Available

Transcripts for HMCN1 Gene

Unigene Clusters for HMCN1 Gene

Hemicentin 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMCN1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^
SP1:
SP2:

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33a · 33b ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49a · 49b
SP1:
SP2: -

Relevant External Links for HMCN1 Gene

GeneLoc Exon Structure for
HMCN1
ECgene alternative splicing isoforms for
HMCN1

Expression for HMCN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMCN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HMCN1 Gene

This gene is overexpressed in Artery - Aorta (x11.5), Artery - Coronary (x5.2), and Esophagus - Muscularis (x4.5).

Protein differential expression in normal tissues from HIPED for HMCN1 Gene

This gene is overexpressed in Urine (47.8) and Bone marrow mesenchymal stem cell (14.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HMCN1 Gene



NURSA nuclear receptor signaling pathways regulating expression of HMCN1 Gene:

HMCN1

SOURCE GeneReport for Unigene cluster for HMCN1 Gene:

Hs.58877

mRNA Expression by UniProt/SwissProt for HMCN1 Gene:

Q96RW7-HMCN1_HUMAN
Tissue specificity: Isoform 1 and isoform 2 are expressed in skin fibroblasts and retinal pigment epithelium (RPE) cells (PubMed:14570714).
genes like me logo Genes that share expression patterns with HMCN1: view

Primer Products

No data available for Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMCN1 Gene

Orthologs for HMCN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMCN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HMCN1 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia HMCN1 34 35
  • 90.97 (n)
cow
(Bos Taurus)
Mammalia HMCN1 34 35
  • 89.58 (n)
mouse
(Mus musculus)
Mammalia Hmcn1 34 16 35
  • 85.9 (n)
rat
(Rattus norvegicus)
Mammalia Hmcn1 34
  • 85.51 (n)
oppossum
(Monodelphis domestica)
Mammalia HMCN1 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HMCN1 35
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMCN1 34 35
  • 73.65 (n)
lizard
(Anolis carolinensis)
Reptilia HMCN1 35
  • 73 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hmcn1 34 35
  • 65.05 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002268 34
  • 41.52 (n)
worm
(Caenorhabditis elegans)
Secernentea him-4 34 35
  • 45.22 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
OneToMany
Species where no ortholog for HMCN1 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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)

Evolution for HMCN1 Gene

ENSEMBL:
Gene Tree for HMCN1 (if available)
TreeFam:
Gene Tree for HMCN1 (if available)

Paralogs for HMCN1 Gene

Paralogs for HMCN1 Gene

(21) SIMAP similar genes for HMCN1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HMCN1: view

Variants for HMCN1 Gene

Sequence variations from dbSNP and Humsavar for HMCN1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121434382 other, Macular degeneration, age-related, 1 (ARMD1) [MIM:603075] 186,178,506(+) AGGAC(A/G)ACATT intron-variant, reference, missense
rs879255520 Pathogenic 186,001,391(+) CACTC(-/C)ATCTC reference, frameshift-variant
rs10157742 Likely benign 186,117,446(+) TTGTT(A/G/T)TTGTT intron-variant
rs1056456 Likely benign 186,190,552(+) AAAGA(C/T)TGCTT intron-variant, utr-variant-3-prime
rs10798035 Likely benign 186,081,285(+) GATAG(A/G)GTGTT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for HMCN1 Gene

Variant ID Type Subtype PubMed ID
dgv235n106 CNV deletion 24896259
dgv479n100 CNV gain 25217958
esv1976790 CNV deletion 18987734
esv2186053 CNV deletion 18987734
esv23364 CNV loss 19812545
esv2347927 CNV deletion 18987734
esv2468461 CNV deletion 19546169
esv2563566 CNV deletion 19546169
esv2572731 CNV deletion 19546169
esv2657798 CNV deletion 23128226
esv2667054 CNV deletion 23128226
esv2720295 CNV deletion 23290073
esv2720306 CNV deletion 23290073
esv2720317 CNV deletion 23290073
esv2720328 CNV deletion 23290073
esv2720339 CNV deletion 23290073
esv3543700 CNV deletion 23714750
esv3588143 CNV loss 21293372
esv3588145 CNV loss 21293372
esv3588146 CNV loss 21293372
esv3890826 CNV gain 25118596
nsv1007237 CNV gain 25217958
nsv1118461 CNV duplication 24896259
nsv1137827 CNV deletion 24896259
nsv1145385 CNV deletion 24896259
nsv3866 CNV insertion 18451855
nsv548398 CNV gain 21841781
nsv946541 CNV duplication 23825009

Variation tolerance for HMCN1 Gene

Residual Variation Intolerance Score: 3.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 19.63; 98.91% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HMCN1 Gene

Human Gene Mutation Database (HGMD)
HMCN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMCN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMCN1 Gene

Disorders for HMCN1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for HMCN1 Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 1
  • macular degeneration, age-related, reduced risk of
postpartum depression
  • maternity blues
basal laminar drusen
  • cuticular drusen
degeneration of macula and posterior pole
  • degeneration of macula and posterior pole of retina
- elite association - COSMIC cancer census association via MalaCards
Search HMCN1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HMCN1_HUMAN
  • Macular degeneration, age-related, 1 (ARMD1) [MIM:603075]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269 PubMed:14570714}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HMCN1

Genetic Association Database (GAD)
HMCN1
Human Genome Epidemiology (HuGE) Navigator
HMCN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMCN1
genes like me logo Genes that share disorders with HMCN1: view

No data available for Genatlas for HMCN1 Gene

Publications for HMCN1 Gene

  1. Evaluation of the ARMD1 locus on 1q25-31 in patients with age-related maculopathy: genetic variation in laminin genes and in exon 104 of HEMICENTIN-1. (PMID: 15370542) Hayashi M. … Allikmets R. (Ophthalmic Genet. 2004) 3 22 46 64
  2. Analysis of the ARMD1 locus: evidence that a mutation in hemicentin-1 is associated with age-related macular degeneration in a large family. (PMID: 14570714) Schultz D.W. … Acott T.S. (Hum. Mol. Genet. 2003) 3 4 22 64
  3. Examination of association with candidate genes for diabetic nephropathy in a Mexican American population. (PMID: 20299368) Kim S. … Adler S.G. (Clin J Am Soc Nephrol 2010) 3 46 64
  4. Fibulin-6 expression and anoikis in human salivary gland epithelial cells: implications in Sjogren's syndrome. (PMID: 19190085) Sisto M. … Lisi S. (Int. Immunol. 2009) 3 22 64
  5. Integrative predictive model of coronary artery calcification in atherosclerosis. (PMID: 19948975) McGeachie M. … Ramoni M.F. (Circulation 2009) 3 46 64

Products for HMCN1 Gene

Sources for HMCN1 Gene

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