LIN7B lin-7 homolog B, crumbs cell polarity complex component [Homo sapiens (human)] - Gene

Summary

Official Symbol: LIN7Bprovided by HGNC
Official Full Name: lin-7 homolog B, crumbs cell polarity complex componentprovided by HGNC
Primary source: HGNC:HGNC:17788
See related: Ensembl:ENSG00000104863 MIM:612331; AllianceGenome:HGNC:17788
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: MALS2; VELI2; LIN-7B; MALS-2
Summary: Enables protein domain specific binding activity. Predicted to be involved in maintenance of epithelial cell apical/basal polarity; neurotransmitter secretion; and protein localization to basolateral plasma membrane. Predicted to be located in plasma membrane. Predicted to be part of MPP7-DLG1-LIN7 complex. Predicted to be active in basolateral plasma membrane; cell-cell junction; and synapse. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in brain (RPKM 4.4), testis (RPKM 3.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (49114370..49118460)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (52109104..52113194)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (49617627..49621717)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

functional deficiency in Lin-7B could be implicated in clinical phenotypes in some autism spectrum disorders patients through bringing about abnormal cortical architecture
Title: Role of an adaptor protein Lin-7B in brain development: possible involvement in autism spectrum disorders.
Data suggest that decreased cortical LIN7b expression may contribute to abnormal corticostriatal connectivity in Huntington disease.
Title: Decreased Lin7b expression in layer 5 pyramidal neurons may contribute to impaired corticostriatal connectivity in huntington disease.
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.
PSD-95 and Lin-7b interact with acid-sensing ion channel-3 and have opposite effects on H+- gated current
Title: PSD-95 and Lin-7b interact with acid-sensing ion channel-3 and have opposite effects on H+- gated current.
LIN7B is a partner of IRSp53 anchoring the actin-based membrane cytoskeleton at cell-cell contacts.
Title: MALS is a binding partner of IRSp53 at cell-cell contacts.
Lin-7B is a binding partner for Rhotekin in the human brain cDNA library
Title: Identification of a cell polarity-related protein, Lin-7B, as a binding partner for a Rho effector, Rhotekin, and their possible interaction in neurons.

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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

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 B (C. elegans) (LIN7B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L27 domain binding	IBA Inferred from Biological aspect of Ancestor more info
enables PDZ domain binding	IEA Inferred from Electronic Annotation more info
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 kinase binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in maintenance of epithelial cell apical/basal polarity	IBA Inferred from Biological aspect of Ancestor more info
involved_in neurotransmitter secretion	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to basolateral plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of MPP7-DLG1-LIN7 complex	IBA Inferred from Biological aspect of Ancestor more info
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 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 B

Names: hLin7B; hVeli2; mammalian lin-seven protein 2; veli-2; vertebrate lin-7 homolog 2

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_001308419.2 → NP_001295348.1 protein lin-7 homolog B isoform 2

See identical proteins and their annotated locations for NP_001295348.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.

Source sequence(s)

AF311862, AY358744, BM069859

Consensus CDS

CCDS77328.1

UniProtKB/Swiss-Prot

Q9HAP6

Related

ENSP00000375737.3, ENST00000391864.7

Conserved Domains (2) summary

pfam02828
Location:14 → 66

L27; L27 domain

cl00117
Location:76 → 102

PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
NM_022165.3 → NP_071448.1 protein lin-7 homolog B isoform 1

See identical proteins and their annotated locations for NP_071448.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AY358744

Consensus CDS

CCDS12757.1

UniProtKB/Swiss-Prot

Q9HAP6

Related

ENSP00000221459.2, ENST00000221459.7

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

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_000019.10 Reference GRCh38.p14 Primary Assembly

Range

49114370..49118460

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017027131.3 → XP_016882620.1 protein lin-7 homolog B isoform X2
XM_006723323.4 → XP_006723386.1 protein lin-7 homolog B isoform X1

Conserved Domains (2) summary

cd00992
Location:67 → 148

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 → 57

L27; L27 domain