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

    Gene ID: 80059, updated on 10-Dec-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, Dec 2024]
    Expression
    Biased expression in brain (RPKM 5.6) and lung (RPKM 0.2) See more
    Orthologs
    mouse all
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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
    • 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 Variation Viewer (GRCh37.p13)

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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