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HMCN1 hemicentin 1 [ Homo sapiens (human) ]

Gene ID: 83872, updated on 2-Nov-2024

Summary

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Official Symbol
HMCN1provided by HGNC
Official Full Name
hemicentin 1provided by HGNC
Primary source
HGNC:HGNC:19194
See related
Ensembl:ENSG00000143341 MIM:608548; AllianceGenome:HGNC:19194
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ARMD1; FBLN6; FIBL6; FIBL-6
Summary
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]
Expression
Broad expression in lung (RPKM 3.2), gall bladder (RPKM 2.4) and 21 other tissues See more
Orthologs
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Genomic context

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See HMCN1 in Genome Data Viewer
Location:
1q25.3-q31.1
Exon count:
108
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (185734391..186190949)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (185089079..185545614)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (185703523..186160081)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985239 Neighboring gene MPRA-validated peak505 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:185554623-185555822 Neighboring gene long intergenic non-protein coding RNA 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2245 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:185615105-185616018 Neighboring gene uncharacterized GS1-204I12.4 Neighboring gene NANOG hESC enhancer GRCh37_chr1:185663280-185663781 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185668941-185669602 Neighboring gene MPRA-validated peak509 silencer Neighboring gene MPRA-validated peak510 silencer Neighboring gene MPRA-validated peak511 silencer Neighboring gene Sharpr-MPRA regulatory region 5860 Neighboring gene MPRA-validated peak512 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185917425-185918340 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:185922788-185923626 Neighboring gene MPRA-validated peak513 silencer Neighboring gene uncharacterized LOC105371654 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:186156636-186157835 Neighboring gene MPRA-validated peak514 silencer Neighboring gene uncharacterized LOC124904471 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:186214031-186214197 Neighboring gene RNA, U6 small nuclear 1240, pseudogene Neighboring gene proteoglycan 4 Neighboring gene translocated promoter region, nuclear basket protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Comprehensive Analysis of HMCN1 Somatic Mutation in Clear Cell Renal Cell Carcinoma. Gong Z, et al. Genes (Basel), 2022 Jul 20. PMID 35886066, Free PMC Article
  2. Case-control genetic association study of fibulin-6 (FBLN6 or HMCN1) variants in age-related macular degeneration (AMD). Fisher SA, et al. Hum Mutat, 2007 Apr. PMID 17216616
  3. Fibulin-6 expression and anoikis in human salivary gland epithelial cells: implications in Sjogren's syndrome. Sisto M, et al. Int Immunol, 2009 Mar. PMID 19190085
  4. A novel diagnostic test detects a low frequency of the hemicentin Gln5345Arg variant among Northern Irish age related macular degeneration patients. McKay GJ, et al. Mol Vis, 2004 Sep 24. PMID 15467524
  5. Analysis of the ARMD1 locus: evidence that a mutation in HEMICENTIN-1 is associated with age-related macular degeneration in a large family. Schultz DW, et al. Hum Mol Genet, 2003 Dec 15. PMID 14570714

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HOXD9 aggravates the development of cervical cancer by transcriptionally activating HMCN1.
    Title: HOXD9 aggravates the development of cervical cancer by transcriptionally activating HMCN1.
  2. Comprehensive Analysis of HMCN1 Somatic Mutation in Clear Cell Renal Cell Carcinoma.
    Title: Comprehensive Analysis of HMCN1 Somatic Mutation in Clear Cell Renal Cell Carcinoma.
  3. the findings of the present study suggest that targeting the Cancerassociated fibroblasts genes, SRPX and HMCN1, can inhibit ovarian cancer migration and invasion.
    Title: SRPX and HMCN1 regulate cancer‑associated fibroblasts to promote the invasiveness of ovarian carcinoma.
  4. Identify HMCN1 as a new molecule involved in the dynamic changes of podocyte foot processes in glomerular disease.
    Title: Hemicentin 1 influences podocyte dynamic changes in glomerular diseases.
  5. In the group that combined individuals affected by isolated cleft lip and palate, tooth agenesis, supernumerary teeth, molar incisor hypomineralization, or dental caries, we found an association with rs622260 but not with the rs10798049 marker. We determined that allele C of rs622260 was overrepresented in all individuals studied compared with a group of unrelated individuals who did not present any of these conditions.
    Title: Rethinking isolated cleft lip and palate as a syndrome.
  6. A null-variant in HMCN1 (c.4162delC), has been identified in a Tunisian Jewish family with early-onset age-related macular degeneration.
    Title: Rare genetic variants in Tunisian Jewish patients suffering from age-related macular degeneration.
  7. HMCN1 mutation is associated with gastric and colorectal cancers.
    Title: HMCN1, a cell polarity-related gene, is somatically mutated in gastric and colorectal cancers.
  8. Fibulin-6, a fibroblast-released extracellular matrix protein, may play an important role during myocardial remodelling by imparting an effect on cardiac fibroblasts migration in close and complementary interplay with TGF-beta1 signalling
    Title: Expression of fibulin-6 in failing hearts and its role for cardiac fibroblast migration.
  9. The identified variants of HMCN1 are on conserved domains, particularly the two variants on calcium-binding epidermal growth factor domain.
    Title: Genome-wide linkage and exome analyses identify variants of HMCN1 for splenic epidermoid cyst.
  10. this is the first association study based on a candidate gene approach to confirm that a HMCN1 polymorphism (rs2891230) is associated with postpartum depression diagnosis. heterozygosity (GA) for this SNP was associated with an increased risk of PPD.
    Title: HMNC1 gene polymorphism associated with postpartum depression.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Age related macular degeneration 1
MedGen: C1864205 OMIM: 603075 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables extracellular matrix structural constituent HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in basement membrane organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to bacterium IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in basement membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cell cortex IEA
Inferred from Electronic Annotation
more info
  
located_in cleavage furrow IEA
Inferred from Electronic Annotation
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with collagen-containing extracellular matrix TAS
Traceable Author Statement
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in extracellular exosome HDA PubMed 
located_in muscle tendon junction ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
hemicentin-1
Names
LOC100507250/HMCN1 fusion
fibulin-6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011841.2 RefSeqGene

    Range
    5002..461560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_031935.3 → NP_114141.2  hemicentin-1 precursor

    See identical proteins and their annotated locations for NP_114141.2

    Status: REVIEWED

    Source sequence(s)
    AL118512, AL121996, AL133515, AL133553, AL135796, AL135797, AL391824, BX928748
    Consensus CDS
    CCDS30956.1
    UniProtKB/Swiss-Prot
    A6NGE3, Q5TYR7, Q96DN3, Q96DN8, Q96RW7, Q96SC3
    Related
    ENSP00000271588.4, ENST00000271588.9
    Conserved Domains (12) summary
    cd00096
    Location:720 → 786
    Ig; Immunoglobulin domain
    smart00408
    Location:2493 → 2557
    IGc2; Immunoglobulin C-2 Type
    smart00179
    Location:5432 → 5471
    EGF_CA; Calcium-binding EGF-like domain
    smart00209
    Location:4646 → 4698
    TSP1; Thrombospondin type 1 repeats
    smart00409
    Location:1086 → 1167
    IG; Immunoglobulin
    smart00410
    Location:2299 → 2380
    IG_like; Immunoglobulin like
    smart00682
    Location:4868 → 5092
    G2F; G2 nidogen domain and fibulin
    cd00054
    Location:5230 → 5263
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam07679
    Location:1171 → 1258
    I-set; Immunoglobulin I-set domain
    pfam07645
    Location:5272 → 5313
    EGF_CA; Calcium-binding EGF domain
    pfam13519
    Location:42 → 212
    VWA_2; von Willebrand factor type A domain
    cl11960
    Location:3244 → 3338
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    185734391..186190949
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510038.4 → XP_011508340.1  hemicentin-1 isoform X1

    UniProtKB/Swiss-Prot
    Q96RW7
    Conserved Domains (12) summary
    cd00096
    Location:720 → 786
    Ig; Immunoglobulin domain
    smart00408
    Location:2493 → 2557
    IGc2; Immunoglobulin C-2 Type
    smart00179
    Location:5315 → 5354
    EGF_CA; Calcium-binding EGF-like domain
    smart00209
    Location:4646 → 4698
    TSP1; Thrombospondin type 1 repeats
    smart00409
    Location:2299 → 2380
    IG; Immunoglobulin
    smart00410
    Location:1086 → 1167
    IG_like; Immunoglobulin like
    smart00682
    Location:4868 → 5092
    G2F; G2 nidogen domain and fibulin
    cd00054
    Location:5230 → 5263
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam07679
    Location:1171 → 1258
    I-set; Immunoglobulin I-set domain
    pfam07645
    Location:5272 → 5313
    EGF_CA; Calcium-binding EGF domain
    pfam13519
    Location:42 → 212
    VWA_2; von Willebrand factor type A domain
    cl11960
    Location:3244 → 3338
    Ig; Immunoglobulin domain

  2. XM_024450118.2 → XP_024305886.1  hemicentin-1 isoform X4

    Conserved Domains (9) summary
    smart00408
    Location:1843 → 1905
    IGc2; Immunoglobulin C-2 Type
    smart00409
    Location:1086 → 1167
    IG; Immunoglobulin
    smart00410
    Location:526 → 608
    IG_like; Immunoglobulin like
    cd00198
    Location:42 → 198
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam07679
    Location:1171 → 1258
    I-set; Immunoglobulin I-set domain
    pfam13927
    Location:2383 → 2461
    Ig_3; Immunoglobulin domain
    cd00096
    Location:3169 → 3235
    Ig; Immunoglobulin domain
    cl11960
    Location:792 → 875
    Ig; Immunoglobulin domain
    cl28434
    Location:1746 → 1822
    I-set; Immunoglobulin I-set domain

  3. XM_011510041.4 → XP_011508343.1  hemicentin-1 isoform X5

    Conserved Domains (7) summary
    cd00096
    Location:720 → 786
    Ig; Immunoglobulin domain
    smart00408
    Location:2493 → 2557
    IGc2; Immunoglobulin C-2 Type
    smart00409
    Location:1086 → 1167
    IG; Immunoglobulin
    smart00410
    Location:799 → 884
    IG_like; Immunoglobulin like
    pfam07679
    Location:1171 → 1258
    I-set; Immunoglobulin I-set domain
    pfam13519
    Location:42 → 212
    VWA_2; von Willebrand factor type A domain
    cl11960
    Location:792 → 884
    Ig; Immunoglobulin domain

  4. XM_017002437.2 → XP_016857926.1  hemicentin-1 isoform X2

  5. XM_047431608.1 → XP_047287564.1  hemicentin-1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    185089079..185545614
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339006.1 → XP_054194981.1  hemicentin-1 isoform X1

  2. XM_054339009.1 → XP_054194984.1  hemicentin-1 isoform X4

  3. XM_054339010.1 → XP_054194985.1  hemicentin-1 isoform X5

  4. XM_054339007.1 → XP_054194982.1  hemicentin-1 isoform X2

  5. XM_054339008.1 → XP_054194983.1  hemicentin-1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96RW7.2 GenPept UniProtKB/Swiss-Prot:Q96RW7

Gene LinkOut

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