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

Summary

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 several cellular components, including Schaffer collateral - CA1 synapse; cell surface; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.2-p21.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (40391591..40587364, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (40219487..40415195, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (40359330..40555103, complement)

Chromosome 6 - NC_000006.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.

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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

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 EBI GWAS CatalogPubMed
Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH78230 (e-PCR)
- UniSTS:31241

RH122955 (e-PCR)
- UniSTS:135252

SHGC-82338 (e-PCR)
- UniSTS:104304

RH98364 (e-PCR)
- UniSTS:86674

D6S1607 (e-PCR)
- UniSTS:50851

RH119972 (e-PCR)
- UniSTS:133295

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 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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

40391591..40587364 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060930.1 Alternate T2T-CHM13v2.0

Range

40219487..40415195 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8V8TQ63