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LRFN1 leucine rich repeat and fibronectin type III domain containing 1 [ Homo sapiens (human) ]

Gene ID: 57622, updated on 11-Apr-2024

Summary

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Official Symbol
LRFN1provided by HGNC
Official Full Name
leucine rich repeat and fibronectin type III domain containing 1provided by HGNC
Primary source
HGNC:HGNC:29290
See related
Ensembl:ENSG00000128011 MIM:612807; AllianceGenome:HGNC:29290
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
SALM2
Summary
Predicted to be involved in regulation of postsynaptic density assembly. Predicted to be located in plasma membrane. Predicted to be active in cell surface. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 2.1), spleen (RPKM 1.1) and 18 other tissues See more
Orthologs
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Genomic context

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See LRFN1 in Genome Data Viewer
Location:
19q13.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39306566..39320863, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42110835..42125134, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39797206..39811503, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene interferon lambda 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39798467-39798968 Neighboring gene interferon lambda 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10596 Neighboring gene glia maturation factor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10597 Neighboring gene sterile alpha motif domain containing 4B Neighboring gene RNA, 7SL, cytoplasmic 566, pseudogene

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. Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data. Ruan B, et al. Dis Markers, 2020. PMID 33110456, Free PMC Article
  2. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. Morimura N, et al. Gene, 2006 Oct 1. PMID 16828986
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
  4. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Matheson NJ, et al. Cell Host Microbe, 2015 Oct 14. PMID 26439863, Free PMC Article
  5. SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation. Shi R, et al. Cell Biosci, 2021 Jul 27. PMID 34315543, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
    Title: Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
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

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LRFN1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1484

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in regulation of postsynaptic density assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in presynaptic active zone membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
leucine-rich repeat and fibronectin type III domain-containing protein 1
Names
CTC-246B18.8
synaptic adhesion-like molecule 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)

  1. NM_020862.2 → NP_065913.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 precursor

    See identical proteins and their annotated locations for NP_065913.1

    Status: VALIDATED

    Source sequence(s)
    AC011445
    Consensus CDS
    CCDS46071.1
    UniProtKB/Swiss-Prot
    Q8TBS9, Q9P244
    Related
    ENSP00000248668.4, ENST00000248668.5
    Conserved Domains (8) summary
    smart00082
    Location:252 → 284
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:310 → 385
    IG_like; Immunoglobulin like
    cd00116
    Location:65 → 174
    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 ...
    sd00033
    Location:67 → 90
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:426 → 500
    fn3; Fibronectin type III domain
    pfam12799
    Location:165 → 203
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:65 → 125
    LRR_8; Leucine rich repeat
    cl11960
    Location:314 → 387
    Ig; Immunoglobulin 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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    39306566..39320863 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027033.2 → XP_016882522.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q8TBS9, Q9P244
    Conserved Domains (8) summary
    smart00082
    Location:252 → 284
    LRRCT; Leucine rich repeat C-terminal domain
    smart00410
    Location:310 → 385
    IG_like; Immunoglobulin like
    cd00116
    Location:65 → 174
    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 ...
    sd00033
    Location:67 → 90
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:426 → 500
    fn3; Fibronectin type III domain
    pfam12799
    Location:165 → 203
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:65 → 125
    LRR_8; Leucine rich repeat
    cl11960
    Location:314 → 387
    Ig; Immunoglobulin domain

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791808.1 Reference GRCh38.p14 PATCHES

    Range
    86948..101245 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333248.1 → XP_054189223.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q8TBS9, Q9P244

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    42110835..42125134 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321546.1 → XP_054177521.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q8TBS9, Q9P244
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P244.2 GenPept UniProtKB/Swiss-Prot:Q9P244

Gene LinkOut

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