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LRFN2 leucine rich repeat and fibronectin type III domain containing 2 [ Homo sapiens (human) ]

Gene ID: 57497, updated on 11-Apr-2024

Summary

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Official Symbol
LRFN2provided by HGNC
Official Full Name
leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
Primary source
HGNC:HGNC:21226
See related
Ensembl:ENSG00000156564 MIM:612808; AllianceGenome:HGNC:21226
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
SALM1; FIGLER2; KIAA1246
Summary
Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Predicted to be located in plasma membrane. Predicted to be active in Schaffer collateral - CA1 synapse and cell surface. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
6p21.2-p21.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (40391591..40587364, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (40219487..40415195, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (40359330..40555103, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40311845-40312560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40313277-40313990 Neighboring gene long intergenic non-protein coding RNA 951 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:40327493-40328118 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:40346056-40347255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40377247-40377748 Neighboring gene testis development related 1 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40386520-40387156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40387157-40387792 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40387793-40388428 Neighboring gene RNA, U6 small nuclear 250, pseudogene Neighboring gene uncharacterized LOC105379699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40477543-40478043 Neighboring gene uncharacterized LOC105375051 Neighboring gene Sharpr-MPRA regulatory region 9042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17170 Neighboring gene uncharacterized LOC101929535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40680899-40681400 Neighboring gene uncharacterized LOC105375052

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. LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir. Shah R, et al. J Cancer Res Ther, 2020 Dec. PMID 32880595
  2. Heterozygous deletion of the LRFN2 gene is associated with working memory deficits. Thevenon J, et al. Eur J Hum Genet, 2016 Jun. PMID 26486473, Free PMC Article
  3. Dileucine and PDZ-binding motifs mediate synaptic adhesion-like molecule 1 (SALM1) trafficking in hippocampal neurons. Seabold GK, et al. J Biol Chem, 2012 Feb 10. PMID 22174418, Free PMC Article
  4. LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway. Zhou Y, et al. Cancer Sci, 2022 Oct. PMID 35879265, Free PMC Article
  5. Genetic variants of DNAH11 and LRFN2 genes and their association with ovarian and breast cancer. Verma S, et al. Int J Gynaecol Obstet, 2020 Jan. PMID 31605628

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8[+] T cell infiltration and functional transition.
    Title: Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8(+) T cell infiltration and functional transition.
  2. LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/beta-Catenin and NF-kappaB signaling pathway.
    Title: LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway.
  3. LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir.
    Title: LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir.
  4. No significant association of variant rs2494938 of LRFN2 was observed with ovarian canceror breast cancer in a cohort of women in India.
    Title: Genetic variants of DNAH11 and LRFN2 genes and their association with ovarian and breast cancer.
  5. study demonstrated that the polymorphisms rs2494938 at 6p21.1 and rs2285947 at 7p15.3 may serve as independent prognostic biomarkers for ESCC, implying the potential biological role of their related genes (LRFN2 and DNAH11) in the process of ESCC development
    Title: Intronic polymorphisms in genes LRFN2 (rs2494938) and DNAH11 (rs2285947) are prognostic indicators of esophageal squamous cell carcinoma.
  6. Microdeletion encompassing LRFN2 gene segregates with working memory deficits and learning disabilities in three family members.
    Title: Heterozygous deletion of the LRFN2 gene is associated with working memory deficits.
  7. enrichment of SALM1 on the cell surface affects dendritic arborization, and intracellular motifs regulate its dendritic versus axonal localization.
    Title: Dileucine and PDZ-binding motifs mediate synaptic adhesion-like molecule 1 (SALM1) trafficking in hippocampal neurons.
  8. 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
A genome-wide association meta-analysis identifies a novel locus at 17q11.2 associated with sporadic amyotrophic lateral sclerosis.
EBI GWAS Catalog
Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in modulation of chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of postsynapse organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
  
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 membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat and fibronectin type-III domain-containing protein 2
Names
fibronectin type III, immunoglobulin and leucine rich repeat domains 2
synaptic adhesion-like molecule 1

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_020737.3 → NP_065788.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor

    See identical proteins and their annotated locations for NP_065788.1

    Status: VALIDATED

    Source sequence(s)
    AB033072, AK291474, AL591063
    Consensus CDS
    CCDS34443.1
    UniProtKB/Swiss-Prot
    A5PKU3, Q5SYP9, Q9ULH4
    UniProtKB/TrEMBL
    A0A8V8TQ63
    Related
    ENSP00000345985.6, ENST00000338305.7
    Conserved Domains (5) summary
    smart00082
    Location:242 → 286
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:54 → 77
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:420 → 493
    fn3; Fibronectin type III domain
    pfam13855
    Location:76 → 136
    LRR_8; Leucine rich repeat
    cl11960
    Location:303 → 376
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    40391591..40587364 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514762.3 → XP_011513064.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011513064.1

    UniProtKB/Swiss-Prot
    A5PKU3, Q5SYP9, Q9ULH4
    UniProtKB/TrEMBL
    A0A8V8TQ63
    Conserved Domains (5) summary
    smart00082
    Location:242 → 286
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:54 → 77
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:420 → 493
    fn3; Fibronectin type III domain
    pfam13855
    Location:76 → 136
    LRR_8; Leucine rich repeat
    cl11960
    Location:303 → 376
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    40219487..40415195 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356062.1 → XP_054212037.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A5PKU3, Q5SYP9, Q9ULH4
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9ULH4.2 GenPept UniProtKB/Swiss-Prot:Q9ULH4

Gene LinkOut

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