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LRRTM4 leucine rich repeat transmembrane neuronal 4 [ Homo sapiens (human) ]

Gene ID: 80059, updated on 2-Nov-2024

Summary

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Official Symbol
LRRTM4provided by HGNC
Official Full Name
leucine rich repeat transmembrane neuronal 4provided by HGNC
Primary source
HGNC:HGNC:19411
See related
Ensembl:ENSG00000176204 MIM:610870; AllianceGenome:HGNC:19411
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
Predicted to enable heparan sulfate proteoglycan binding activity. Predicted to be involved in regulation of synapse assembly. Predicted to act upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Predicted to be located in postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in several cellular components, including GABA-ergic synapse; photoreceptor ribbon synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 5.6) and lung (RPKM 0.2) See more
Orthologs
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Genomic context

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See LRRTM4 in Genome Data Viewer
Location:
2p12
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (76747685..77522376, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (76752924..77527386, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (76974811..77749502, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374814 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:76800731-76801627 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:76806283-76806782 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:76806783-76807284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:76829490-76830118 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:76851459-76852104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:76880783-76881331 Neighboring gene RN7SK pseudogene 164 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:77008030-77008622 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:77023220-77023770 Neighboring gene uncharacterized LOC105374815 Neighboring gene RNA, 5S ribosomal pseudogene 98 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:77245203-77245860 Neighboring gene LRRTM4 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:77314877-77315380 Neighboring gene 2p12 distal HERV-mediated recombination region Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:77315381-77315885 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:77319973-77320736 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:77320737-77321498 Neighboring gene NANOG hESC enhancer GRCh37_chr2:77614348-77614916 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:77648449-77648664 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:77749816-77750481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:77817198-77817735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:77817736-77818272 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:77820253-77820819 Neighboring gene tRNA-Pro (anticodon AGG) 5-1 Neighboring gene uncharacterized LOC101927967 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:77981196-77981732 Neighboring gene RPL38 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. LRRTM4 Terminal Exon Duplicated in Family with Tourette Syndrome, Autism and ADHD. Clarke RA, et al. Genes (Basel), 2021 Dec 27. PMID 35052406, Free PMC Article
  2. Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. Reichman RD, et al. Am J Med Genet B Neuropsychiatr Genet, 2020 Mar. PMID 31854516, Free PMC Article
  3. Unbiased discovery of glypican as a receptor for LRRTM4 in regulating excitatory synapse development. de Wit J, et al. Neuron, 2013 Aug 21. PMID 23911103, Free PMC Article
  4. A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. Laurén J, et al. Genomics, 2003 Apr. PMID 12676565
  5. PTPσ functions as a presynaptic receptor for the glypican-4/LRRTM4 complex and is essential for excitatory synaptic transmission. Ko JS, et al. Proc Natl Acad Sci U S A, 2015 Feb 10. PMID 25624497, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LRRTM4 Terminal Exon Duplicated in Family with Tourette Syndrome, Autism and ADHD.
    Title: LRRTM4 Terminal Exon Duplicated in Family with Tourette Syndrome, Autism and ADHD.
  2. Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder.
    Title: Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12568, MGC120633, MGC120636

Gene Ontology Provided by GOA

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
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat transmembrane neuronal protein 4

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

  1. NG_053082.1 RefSeqGene

    Range
    5058..779749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001134745.3 → NP_001128217.1  leucine-rich repeat transmembrane neuronal protein 4 isoform a precursor

    See identical proteins and their annotated locations for NP_001128217.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) and variant 3 encode the same isoform (a).
    Source sequence(s)
    AC068616, AI079273, AK126961, AY358324
    Consensus CDS
    CCDS46346.1
    UniProtKB/Swiss-Prot
    Q4FZ98, Q6UXJ7, Q86VH4
    UniProtKB/TrEMBL
    B3KV11
    Related
    ENSP00000387297.1, ENST00000409884.6
    Conserved Domains (3) summary
    sd00031
    Location:303 → 315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:64 → 86
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:133 → 193
    LRR_8; Leucine rich repeat

  2. NM_001282924.3 → NP_001269853.1  leucine-rich repeat transmembrane neuronal protein 4 isoform a precursor

    See identical proteins and their annotated locations for NP_001269853.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same isoform a.
    Source sequence(s)
    AC068616, AC079614, AI079273, AK122612, AY358324
    Consensus CDS
    CCDS46346.1
    UniProtKB/Swiss-Prot
    Q4FZ98, Q6UXJ7, Q86VH4
    UniProtKB/TrEMBL
    B3KV11
    Related
    ENSP00000386357.1, ENST00000409093.1
    Conserved Domains (3) summary
    sd00031
    Location:303 → 315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:64 → 86
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:133 → 193
    LRR_8; Leucine rich repeat

  3. NM_001282928.3 → NP_001269857.1  leucine-rich repeat transmembrane neuronal protein 4 isoform c precursor

    See identical proteins and their annotated locations for NP_001269857.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' region and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR. It initiates translation at an alternate start codon compared to variant 1 and encodes isoform c, which distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AC079614, AK122612, BC098301
    Consensus CDS
    CCDS74530.1
    UniProtKB/TrEMBL
    Q4KMX1, Q6ZT31
    Related
    ENSP00000386286.1, ENST00000409282.1
    Conserved Domains (3) summary
    sd00031
    Location:304 → 316
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:65 → 87
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:134 → 194
    LRR_8; Leucine rich repeat

  4. NM_001330370.2 → NP_001317299.1  leucine-rich repeat transmembrane neuronal protein 4 isoform d precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' region and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is longer than isoform a.
    Source sequence(s)
    AC068616, AC079614
    Consensus CDS
    CCDS82475.1
    UniProtKB/TrEMBL
    B3KV11, B8ZZ84
    Related
    ENSP00000387228.1, ENST00000409911.5
    Conserved Domains (4) summary
    cd00116
    Location:85 → 291
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00031
    Location:304 → 316
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:65 → 87
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:134 → 194
    LRR_8; Leucine rich repeat

  5. NM_024993.6 → NP_079269.4  leucine-rich repeat transmembrane neuronal protein 4 isoform b precursor

    See identical proteins and their annotated locations for NP_079269.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks the 3' terminal exon and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform b which is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC079614
    Consensus CDS
    CCDS46347.1
    UniProtKB/TrEMBL
    Q6ZT31
    Related
    ENSP00000386236.3, ENST00000409088.3
    Conserved Domains (3) summary
    sd00031
    Location:303 → 315
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:64 → 86
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:90 → 311
    PPP1R42; protein phosphatase 1 regulatory subunit 42

RNA

  1. NR_146416.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC068616, AC079614

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    76747685..77522376 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    76752924..77527386 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86VH4.2 GenPept UniProtKB/Swiss-Prot:Q86VH4

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