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 ... See more...

Aliases for HMCN1 Gene

Aliases for HMCN1 Gene

  • Hemicentin 1 2 3 5
  • Hemicentin-1 3 4
  • Fibulin-6 3 4
  • FIBL-6 3 4
  • FIBL6 3 4
  • Age-Related Macular Degeneration 1 (Senile Macular Degeneration) 2
  • LOC100507250/HMCN1 Fusion 3
  • EC 2.7.10.1 52
  • EC 3.6.5.5 52
  • 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
  • GC01P185703
  • 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 Cardiomyopathy, Dilated, 1L. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is OBSCN.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for HMCN1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMCN1 Gene

Genomics for HMCN1 Gene

GeneHancer (GH) Regulatory Elements for HMCN1 Gene

Promoters and enhancers for HMCN1 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
GH01J185733 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +1.0 954 3.9 ZNF217 CTCF ZNF639 ZNF10 ZIC2 ZBTB10 ZBTB26 EP300 ZEB1 HDAC2 HMCN1 PDC-AS1 ENSG00000228238 ENSG00000233196 lnc-HMCN1-3 piR-32470-005
GH01J185693 Enhancer 0.7 ENCODE 18 -40.1 -40099 1.2 ZBTB40 ZBTB11 POLR2A FOXA2 RELA GABPA SRF SPI1 GABPB1 NR2F2 HMCN1 lnc-HMCN1-3 piR-39098-016
GH01J186081 Enhancer 1.4 FANTOM5 Ensembl ENCODE 9.2 +348.3 348293 2.1 ZNF217 ZSCAN5C GTF2E2 ZNF639 ZBTB5 ZIC2 AFF1 TRIM28 REST HES1 HMCN1 PDC piR-40678-001 piR-32559-026
GH01J185861 Enhancer 1 FANTOM5 Ensembl 10.7 +127.9 127920 1.8 HES1 EP300 ZNF316 TCF7L2 TRIM24 NCOR1 PBX2 JUN NFE2 FOSL1 HMCN1 piR-32470-005 piR-41245-021
GH01J185767 Enhancer 0.5 Ensembl 18.4 +33.5 33520 0.6 OSR2 ZNF843 BCL11B PRDM6 ZNF18 FEZF1 TRIM28 KLF10 MZF1 SCRT2 HMCN1 piR-32470-005
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMCN1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMCN1

Top Transcription factor binding sites by QIAGEN in the HMCN1 gene promoter:
  • AREB6
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXO1a
  • Lhx3a
  • LHX3b
  • Nkx2-5
  • PPAR-alpha
  • TBP
  • TFIID

Genomic Locations for HMCN1 Gene

Genomic Locations for HMCN1 Gene
chr1:185,734,381-186,190,953
(GRCh38/hg38)
Size:
456,573 bases
Orientation:
Plus strand
chr1:185,703,683-186,160,085
(GRCh37/hg19)
Size:
456,403 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; 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 Asn620, Asn693, Asn809, Asn349, Asn970, Asn390, Asn528, Asn1158, Asn550, Asn573, Asn1272, Asn1369, Asn1552, Asn1929, Asn2112, Asn2155, Asn2395, Asn2689, Asn2887, Asn2973, Asn3221, Asn3300, Asn3530, Asn3689, Asn3727, Asn3812, Asn4029, Asn4401, Asn4491, Asn4606, Asn4894, Asn5040, Asn5267, and Asn5615
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • HMCN1_HUMAN (1306)

Other Protein References for HMCN1 Gene

Domains & Families for HMCN1 Gene

Gene Families for HMCN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for HMCN1 Gene

Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin I-set
  • Aspartic acid and asparagine hydroxylation site
  • EGF-like calcium-binding
  • Cadherin
  • Cecropin
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMCN1 Gene

GenScript: Design optimal peptide antigens:
  • Fibulin-6 (HMCN1_HUMAN)
  • Hemicentin 1 (Q5TCP6_HUMAN)
genes like me logo Genes that share domains with HMCN1: view

No data available for Graphical View of Domain Structure and 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

Phenotypes From GWAS Catalog for HMCN1 Gene

Gene Ontology (GO) - Molecular Function for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent HDA 28344315
GO:0005509 calcium ion binding IEA --
GO:0038023 signaling receptor activity IBA 21873635
GO:0042803 protein homodimerization activity IBA 21873635
GO:0050839 cell adhesion molecule binding IBA 21873635
genes like me logo Genes that share ontologies with HMCN1: view
genes like me logo Genes that share phenotypes with HMCN1: view

Human Phenotype Ontology for HMCN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMCN1

No data available for 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
plasma membrane 4
extracellular 4
nucleus 2
cytoskeleton 1
mitochondrion 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005604 basement membrane IEA --
GO:0005737 cytoplasm IEA --
GO:0005913 cell-cell adherens junction IBA 21873635
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with HMCN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMCN1 Gene

Pathways & Interactions for HMCN1 Gene

PathCards logo

SuperPathways for HMCN1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMCN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IBA 21873635
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA 21873635
GO:0007601 visual perception IEA --
GO:0009617 response to bacterium 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

mRNA/cDNA for HMCN1 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMCN1

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

Expression for HMCN1 Gene

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



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

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 31 30
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HMCN1 31 30
  • 90.97 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HMCN1 31 30
  • 89.58 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Hmcn1 17 31 30
  • 85.9 (n)
rat
(Rattus norvegicus)
Mammalia Hmcn1 30
  • 85.51 (n)
oppossum
(Monodelphis domestica)
Mammalia HMCN1 31
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HMCN1 31
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMCN1 31 30
  • 73.65 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HMCN1 31
  • 73 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hmcn1 31 30
  • 65.05 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002268 30
  • 41.52 (n)
worm
(Caenorhabditis elegans)
Secernentea him-4 31 30
  • 45.22 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for HMCN1: view image

Paralogs for HMCN1 Gene

Paralogs for HMCN1 Gene

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

  • HMCN1_HUMAN
  • Q5TCP6_HUMAN
genes like me logo Genes that share paralogs with HMCN1: view

Variants for HMCN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMCN1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
709581 Benign: not provided 186,182,191(+) G/A MISSENSE_VARIANT
709714 Likely Benign: not provided 186,041,119(+) T/A MISSENSE_VARIANT
711056 Likely Benign: not provided 186,166,883(+) G/A MISSENSE_VARIANT
712026 Likely Benign: not provided 186,001,671(+) A/G SYNONYMOUS_VARIANT
719866 Likely Benign: not provided 186,114,053(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for HMCN1 Gene

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)

Additional Variant Information for HMCN1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for HMCN1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for HMCN1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 1
  • macular degeneration, age-related, 2
cardiomyopathy, dilated, 1l
  • cmd1l
postpartum depression
  • maternity blues
basal laminar drusen
  • drusen of bruch membrane
fraser syndrome 1
  • frasrs1
- 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.

Additional Disease Information for HMCN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 genetics 2004) 3 23 41 54
  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 DW … Acott TS (Human molecular genetics 2003) 3 4 23 54
  3. Examination of association with candidate genes for diabetic nephropathy in a Mexican American population. (PMID: 20299368) Kim S … Adler SG (Clinical journal of the American Society of Nephrology : CJASN 2010) 3 41 54
  4. Integrative predictive model of coronary artery calcification in atherosclerosis. (PMID: 19948975) McGeachie M … Ramoni MF (Circulation 2009) 3 41 54
  5. Anti-Ro/SSA autoantibody-mediated regulation of extracellular matrix fibulins in human epithelial cells of the salivary gland. (PMID: 19229767) Lisi S … Sisto M (Scandinavian journal of rheumatology 2009) 3 23 54

Products for HMCN1 Gene

Sources for HMCN1 Gene