LYNX1 Ly6/neurotoxin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LYNX1provided by HGNC
Official Full Name: Ly6/neurotoxin 1provided by HGNC
Primary source: HGNC:HGNC:29604
See related: Ensembl:ENSG00000180155 MIM:606110; AllianceGenome:HGNC:29604
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
Summary: This gene encodes a GPI-anchored, cell membrane bound member of the Ly6/uPAR (LU) superfamily of proteins containing the unique three-finger LU domain. This protein interacts with nicotinic acetylcholine receptors (nAChRs), and is thought to function as a modulator of nAChR activity to prevent excessive excitation. Alternatively spliced transcript variants have been found for this gene. Read-through transcription between this gene and the neighboring downstream gene (SLURP2) generates naturally-occurring transcripts (LYNX1-SLURP2) that encode a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Sep 2017]
Expression: Broad expression in brain (RPKM 28.8), heart (RPKM 21.3) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q24.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (142771197..142777872, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (143914639..143921325, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (143852615..143859288, complement)

Chromosome 8 - NC_000008.11 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 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?

Lynx1 and the family of endogenous mammalian neurotoxin-like proteins and their roles in modulating nAChR function.
Title: Lynx1 and the family of endogenous mammalian neurotoxin-like proteins and their roles in modulating nAChR function.
Spatial Structure and Activity of Synthetic Fragments of Lynx1 and of Nicotinic Receptor Loop C Models.
Title: Spatial Structure and Activity of Synthetic Fragments of Lynx1 and of Nicotinic Receptor Loop C Models.
Increased Expression of LYNX1 in Ovarian Serous Cystadenocarcinoma Predicts Poor Prognosis.
Title: Increased Expression of LYNX1 in Ovarian Serous Cystadenocarcinoma Predicts Poor Prognosis.
The ability of ws-Lynx1 to regulate homeostasis of epithelial cancer cells.
Title: Water-soluble variant of human Lynx1 induces cell cycle arrest and apoptosis in lung cancer cells via modulation of α7 nicotinic acetylcholine receptors.
results show that some functional and behavioral aspects of alpha6-nAChRs are modulated by lynx1
Title: Deletion of lynx1 reduces the function of α6* nicotinic receptors.
These findings provide new insights into the acetylcholine receptor-mediated regulatory mechanism of SLURP-2 expression in keratinocytes.
Title: Transcriptional regulation of SLURP2, a psoriasis-associated gene, is under control of IL-22 in the skin: A special reference to the nested gene LYNX1.
These studies suggest that lynx1 is a potential target both for development of drugs that may limit lung cancer growth as well as for drugs that may be effective for asthma or COPD treatment.
Title: Role of Lynx1 and related Ly6 proteins as modulators of cholinergic signaling in normal and neoplastic bronchial epithelium.
This epigenome-wide DNA methylation analysis in postmortem hippocampus and prefrontal cortex specimens confirmed LYNX1 DNA methylation profiles in major depression.
Title: Aberrant NMDA receptor DNA methylation detected by epigenome-wide analysis of hippocampus and prefrontal cortex in major depression.
Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for alpha-bungarotoxin and similar snake alpha-neurotoxins also targeting alpha7 nAChR.
Title: Water-soluble LYNX1 residues important for interaction with muscle-type and/or neuronal nicotinic receptors.
Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding.
Title: NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-145591 (e-PCR)
- UniSTS:174668

WI-19719 (e-PCR)
- UniSTS:55656

RH80085 (e-PCR)
- UniSTS:88445

RH16413 (e-PCR)
- UniSTS:54410

RH79201 (e-PCR)
- UniSTS:91322

Readthrough LYNX1-SLURP2

Readthrough gene: LYNX1-SLURP2, Included gene: SLURP2

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acetylcholine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables acetylcholine receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables acetylcholine receptor inhibitor activity	IEA Inferred from Electronic Annotation more info
enables acetylcholine receptor regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables acetylcholine receptor regulator activity	IDA Inferred from Direct Assay more info	PubMed
enables ion channel inhibitor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in acetylcholine receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neurotransmitter receptor activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neurotransmitter receptor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic transmission, cholinergic	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ly-6/neurotoxin-like protein 1

Names: Ly-6 neurotoxin-like protein 1; endogenous prototoxin LYNX1; testicular tissue protein Li 112

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_001356370.1 → NP_001343299.1 ly-6/neurotoxin-like protein 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.

Source sequence(s)

AC083841, AF321824, BF994257, BU683767

Consensus CDS

CCDS6389.1

UniProtKB/Swiss-Prot

A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9

Conserved Domains (1) summary

cd00117
Location:21 → 93

LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...
NM_177457.5 → NP_803252.1 ly-6/neurotoxin-like protein 1 precursor

See identical proteins and their annotated locations for NP_803252.1

Status: REVIEWED

Description

Transcript Variant:This variant (3) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.

Source sequence(s)

AC083841, AF321824, BU683767

Consensus CDS

CCDS6389.1

UniProtKB/Swiss-Prot

A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9

Related

ENSP00000478390.1, ENST00000621401.4

Conserved Domains (1) summary

cd00117
Location:21 → 93

LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...
NM_177476.4 → NP_803429.1 ly-6/neurotoxin-like protein 1 precursor

See identical proteins and their annotated locations for NP_803429.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. Variants 1-4 encode the same protein.

Source sequence(s)

AC083841, BG701653, BM172253, BU683767

Consensus CDS

CCDS6389.1

UniProtKB/Swiss-Prot

A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9

Related

ENSP00000478402.1, ENST00000620006.4

Conserved Domains (1) summary

cd00117
Location:21 → 93

LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...
NM_177477.4 → NP_803430.1 ly-6/neurotoxin-like protein 1 precursor

See identical proteins and their annotated locations for NP_803430.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1-4 encode the same protein.

Source sequence(s)

AC083841, BU683767, HY110957

Consensus CDS

CCDS6389.1

UniProtKB/Swiss-Prot

A0A140VJN6, D3DWI7, G3XAC2, P0DP58, Q86SR0, Q9BZG9

Related

ENSP00000498325.1, ENST00000652477.1

Conserved Domains (1) summary

cd00117
Location:21 → 93

LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...