LRRTM3 leucine rich repeat transmembrane neuronal 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LRRTM3provided by HGNC
Official Full Name: leucine rich repeat transmembrane neuronal 3provided by HGNC
Primary source: HGNC:HGNC:19410
See related: Ensembl:ENSG00000198739 MIM:610869; AllianceGenome:HGNC:19410
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
Summary: Involved in presynapse assembly. Acts upstream of or within positive regulation of amyloid-beta formation. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in brain (RPKM 4.5), adrenal (RPKM 1.0) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q21.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (66926036..67101551)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (67789258..67964743)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (68685794..68861309)

Chromosome 10 - NC_000010.11 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 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?

LRRTM3 polymorphisms may play a role in the pathogenesis of late-onset Alzheimer's disease (LOAD) in a Northern Han Chinese population.
Title: Association of LRRTM3 polymorphisms with late-onset Alzheimer's disease in Han Chinese.
protein interactions between LRRTM3, APP and BACE1, as well as complex associations between mRNA levels of LRRTM3, CTNNA3, APP and BACE1 in humans might influence APP metabolism and ultimately risk of AD
Title: LRRTM3 interacts with APP and BACE1 and has variants associating with late-onset Alzheimer's disease (LOAD).
LRRTM3 is not an essential regulator of amyloid-beta production in adult mice; there are no differences in genotype between levels of Abeta or Abeta protein precursor C-terminal fragments in vivo.
Title: LRRTM3 is dispensable for amyloid-β production in mice.
One single-nucleotide polymorphism in the promoter region and a block of 4 single-nucleotide polymorphisms in intron 2 were associated with AD in the National Institute on Aging Late-Onset Alzheimer's Disease data set or the Caribbean Hispanic data set.
Title: Effect of genetic variation in LRRTM3 on risk of Alzheimer disease.
Apart from the complexity of its regulation, alterations in both CTNNA3 and LRTMM3 are implicated in human disease.
Title: Alpha T-catenin (CTNNA3): a gene in the hand is worth two in the nest.
An ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3 in Alzheimer disease.
Title: An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry.
Data suggest that LRRTM3 is a functional and positional candidate gene for Alzheimer disease, and, given its receptor-like structure and restricted expression, a potential therapeutic target.
Title: LRRTM3 promotes processing of amyloid-precursor protein by BACE1 and is a positional candidate gene for late-onset Alzheimer's disease.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CGR167 (e-PCR)
- UniSTS:465434

SHGC-147682 (e-PCR)
- UniSTS:175952

SHGC-80827 (e-PCR)
- UniSTS:102485

WI-22233 (e-PCR)
- UniSTS:70287

STS-AA009437 (e-PCR)
- UniSTS:46777

RH120716 (e-PCR)
- UniSTS:132797

STS-Z39591 (e-PCR)
- UniSTS:13511

SHGC-84525 (e-PCR)
- UniSTS:102868

HSC1UA032 (e-PCR)
- UniSTS:78317

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
acts_upstream_of_or_within positive regulation of amyloid-beta formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: leucine-rich repeat transmembrane neuronal protein 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_178011.5 → NP_821079.3 leucine-rich repeat transmembrane neuronal protein 3 precursor

See identical proteins and their annotated locations for NP_821079.3

Status: VALIDATED

Description

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

Source sequence(s)

AC022401, AC069536, BC111492

Consensus CDS

CCDS7270.1

UniProtKB/Swiss-Prot

A8K2A3, Q2NKX7, Q6N0A3, Q86VH5

Related

ENSP00000355187.3, ENST00000361320.5

Conserved Domains (4) summary

smart00013
Location:33 → 61

LRRNT; Leucine rich repeat N-terminal domain

sd00033
Location:66 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:86 → 145

LRR_8; Leucine rich repeat

cd21340
Location:156 → 342

PPP1R42; protein phosphatase 1 regulatory subunit 42

RNA

NR_111909.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two exons and contains two alternate 5' exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.

Source sequence(s)

AC022401, BU154601, DB029785