LIN7C lin-7 homolog C, crumbs cell polarity complex component [Homo sapiens (human)] - Gene

Summary

Official Symbol: LIN7Cprovided by HGNC
Official Full Name: lin-7 homolog C, crumbs cell polarity complex componentprovided by HGNC
Primary source: HGNC:HGNC:17789
See related: Ensembl:ENSG00000148943 MIM:612332; AllianceGenome:HGNC:17789
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MALS3; VELI3; LIN-7C; MALS-3; LIN-7-C
Summary: Enables L27 domain binding activity and cytoskeletal protein binding activity. Involved in morphogenesis of an epithelial sheet. Located in cell-cell junction; cytoplasm; and plasma membrane. Part of MPP7-DLG1-LIN7 complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in thyroid (RPKM 9.8), liver (RPKM 7.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p14.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (27494418..27506769, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (27634869..27647239, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (27515965..27528316, complement)

Chromosome 11 - NC_000011.10 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 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?

Data show that mirtazapine caused substantial up-regulation of the Lin-7C/beta-catenin pathway in a metastatic squamous cell carcinomas (hSCCs) cell line and melanoma-derived cell line.
Title: Suppression of metastasis by mirtazapine via restoration of the Lin-7C/β-catenin pathway in human cancer cells.
The Dlg1-MPP7-Mals3 heterotrimer consists of 2 pairs of heterodimeric L27 domains. These 2 dimers are asymmetric due to the large difference between the N- and C-terminal tandem L27 domain of MPP7.
Title: Structural basis for tandem L27 domain-mediated polymerization.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Implication of genetic variants near NEGR1, SEC16B, TMEM18, ETV5/DGKG, GNPDA2, LIN7C/BDNF, MTCH2, BCDIN3D/FAIM2, SH2B1, FTO, MC4R, and KCTD15 with obesity and type 2 diabetes in 7705 Chinese.
Allelic and haplotype association was found between both BDNF and adult ADHD, and LIN-7 and adult ADHD.
Title: Association study of brain-derived neurotrophic factor (BDNF) and LIN-7 homolog (LIN-7) genes with adult attention-deficit/hyperactivity disorder.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association study of theta EEG asymmetry and brain-derived neurotrophic factor gene variants in childhood-onset mood disorder.
Overexpression of the Lin-7C gene in an OSCC cell clone does not contribute to underproliferation but results in a noninvasive phenotype with elevated beta-catenin expression.
Title: Lin-7C/VELI3/MALS-3: an essential component in metastasis of human squamous cell carcinoma.
analysis of the solution structure of the heterodimer composed of the L27 domains from LIN-2 and LIN-7
Title: A general model for preferential hetero-oligomerization of LIN-2/7 domains: mechanism underlying directed assembly of supramolecular signaling complexes.
LIN7C is a PDZ protein that interacts with human papillomavirus-16 E6 and forms a tripartite complex with MPP7 and DLG1, regulating the stability and localization of DLG1 to cell junctions.
Title: The stardust family protein MPP7 forms a tripartite complex with LIN7 and DLG1 that regulates the stability and localization of DLG1 to cell junctions.

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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

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of lin-7 homolog C (C. elegans, LIN7C) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17417 (e-PCR)
- UniSTS:2311

D8S2279 (e-PCR)
- UniSTS:473907

D11S1220 (e-PCR)
- UniSTS:15932

A006U38 (e-PCR)
- UniSTS:35174

D11S4549 (e-PCR)
- UniSTS:42436

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L27 domain binding	IDA Inferred from Direct Assay more info	PubMed
enables cytoskeletal protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in morphogenesis of an epithelial sheet	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurotransmitter secretion	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic assembly at neuromuscular junction	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of MPP7-DLG1-LIN7 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MPP7-DLG1-LIN7 complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in basolateral plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protein lin-7 homolog C

Names: LIN-7 protein 3; mammalian lin-seven protein 3; veli-3; vertebrate lin-7 homolog 3

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.

mRNA and Protein(s)

NM_018362.4 → NP_060832.1 protein lin-7 homolog C

See identical proteins and their annotated locations for NP_060832.1

Status: VALIDATED

Source sequence(s)

AK025540, BC039459, BC053907, DA231006

Consensus CDS

CCDS7864.1

UniProtKB/Swiss-Prot

Q9NUP9

UniProtKB/TrEMBL

Q53FX5

Related

ENSP00000278193.2, ENST00000278193.7

Conserved Domains (2) summary

cd00992
Location:91 → 172

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam02828
Location:14 → 66

L27; L27 domain