HMCN1 hemicentin 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 1q25.3-q31.1

Exon count:: 108

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (185734391..186190949)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (185089079..185545614)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (185703523..186160081)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HOXD9 aggravates the development of cervical cancer by transcriptionally activating HMCN1.
Title: HOXD9 aggravates the development of cervical cancer by transcriptionally activating HMCN1.
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.
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.
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.
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.
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.
HMCN1 mutation is associated with gastric and colorectal cancers.
Title: HMCN1, a cell polarity-related gene, is somatically mutated in gastric and colorectal cancers.
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.
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.
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	Compare labs

EBI GWAS Catalog

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

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

D1S191 (e-PCR), detects polymorphism
- UniSTS:19495

SHGC-3550 (e-PCR)
- UniSTS:86862

SHGC-1041 (e-PCR)
- UniSTS:92258

D1S1194 (e-PCR), detects polymorphism
- UniSTS:149361

D1S2165 (e-PCR)
- UniSTS:81013

SHGC-106819 (e-PCR)
- UniSTS:181890

SHGC-106463 (e-PCR)
- UniSTS:169871

D1S413 (e-PCR), detects polymorphism
- UniSTS:48280

SHGC-58126 (e-PCR)
- UniSTS:25758

D1S191 (e-PCR), detects polymorphism
- UniSTS:72894

D1S254 (e-PCR), detects polymorphism
- UniSTS:7107

D1S444 (e-PCR), detects polymorphism
- UniSTS:22728

D1S2848 (e-PCR), detects polymorphism
- UniSTS:18925

AL009939 (e-PCR)
- UniSTS:62189

D1S466 (e-PCR), detects polymorphism
- UniSTS:25075

AB056375 (e-PCR)
- UniSTS:479738

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 more info	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 cycle	IEA Inferred from Electronic Annotation 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 more info	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 more info	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

NG_011841.2 RefSeqGene

Range

5002..461560

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

185734391..186190949

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
XM_017002437.2 → XP_016857926.1 hemicentin-1 isoform X2
XM_047431608.1 → XP_047287564.1 hemicentin-1 isoform X3