LRFN5 leucine rich repeat and fibronectin type III domain containing 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LRFN5provided by HGNC
Official Full Name: leucine rich repeat and fibronectin type III domain containing 5provided by HGNC
Primary source: HGNC:HGNC:20360
See related: Ensembl:ENSG00000165379 MIM:612811; AllianceGenome:HGNC:20360
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SALM5; FIGLER8; C14orf146
Summary: This gene encodes a protein that belongs to the leucine-rich repeat and fibronectin type III domain-containing family of proteins. A similar protein in mouse, a glycosylated transmembrane protein, is thought to function in presynaptic differentiation. [provided by RefSeq, Sep 2016]
Expression: Biased expression in brain (RPKM 2.4), adrenal (RPKM 0.8) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q21.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (41606876..41904549)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (35797646..36095321)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (42076079..42373752)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study.
Title: LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study.
CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
Title: CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions.
Title: LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions.
Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5.
Title: Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5.
we found that chr14.232.a increases expression of LRFN5 in his fibroblasts. Reduced expression of LRFN5 in fibroblasts should be interpreted with caution as these cells might not be representative of expression in brain cells, which are involved in the neurodevelopmental phenotype.
Title: Microdeletion of pseudogene chr14.232.a affects LRFN5 expression in cells of a patient with autism spectrum disorder.
Presynaptic differentiation induced by protein tyrosine phosphatase receptor type D (PTPdelta)-leucine rich repeat and fibronectin type III domain containing 5 (SALM5) requires the dimeric property of SALM5.
Title: Structural basis of trans-synaptic interactions between PTPδ and SALMs for inducing synapse formation.
In the 2:2 heterotetrameric SALM5/PTPdelta complex, a SALM5 dimer bridges two separate PTPdelta molecules.
Title: Structural basis of SALM5-induced PTPδ dimerization for synaptic differentiation.
SALM5/Lrfn5, has recently been implicated in severe progressive autism and familial schizophrenia, pointing to the clinical importance of SALMs.[review]
Title: The SALM/Lrfn family of leucine-rich repeat-containing cell adhesion molecules.
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.
Expression of SALM family proteins SALM3 and SALM5 in nonneural and neural cells induces both excitatory and inhibitory presynaptic differentiation in contacting axons.
Title: Selected SALM (synaptic adhesion-like molecule) family proteins regulate synapse formation.

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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
Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project. 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

MARC_17372-17373:1021901358:1 (e-PCR)
- UniSTS:268288

G63641 (e-PCR)
- UniSTS:140603

SHGC-85115 (e-PCR)
- UniSTS:103488

RH48353 (e-PCR)
- UniSTS:19790

SHGC-83626 (e-PCR)
- UniSTS:100960

SHGC-31628 (e-PCR)
- UniSTS:12521

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of macrophage activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of presynapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic membrane adhesion	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density 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 5

Names: fibronectin type III, immunoglobulin and leucine rich repeat domains 8

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

NG_051660.1 RefSeqGene

Range

5021..302694

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001330106.2 → NP_001317035.1 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.

Source sequence(s)

AL109662, AL121821, AL138498, AW013887

Consensus CDS

CCDS81800.1

UniProtKB/TrEMBL

G3V364, G3V4N1

Related

ENSP00000451067.1, ENST00000554171.1

Conserved Domains (6) summary

cd05764
Location:301 → 374

Ig_2; Subgroup of the immunoglobulin (Ig) superfamily

cd00116
Location:41 → 207

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 ...

pfam07679
Location:287 → 374

I-set; Immunoglobulin I-set domain

sd00033
Location:53 → 76

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:99 → 159

LRR_8; Leucine rich repeat

cl15307
Location:240 → 272

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
NM_001346173.2 → NP_001333102.1 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR comapred to variant 1. Variants 1 and 3 encode the same isoform (1).

Source sequence(s)

AL121821, AL138498, AW013887

Consensus CDS

CCDS9678.1

UniProtKB/Swiss-Prot

B3KU78, Q86XL2, Q96NI6

UniProtKB/TrEMBL

B4DS98
NM_001346175.2 → NP_001333104.1 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.

Source sequence(s)

AL121821, AL138498, AW013887

Consensus CDS

CCDS81800.1

UniProtKB/TrEMBL

G3V364, G3V4N1
NM_152447.5 → NP_689660.2 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

See identical proteins and their annotated locations for NP_689660.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.

Source sequence(s)

AK096627, AL121821, AL138498, AW013887, BC043165, DA096504

Consensus CDS

CCDS9678.1

UniProtKB/Swiss-Prot

B3KU78, Q86XL2, Q96NI6

UniProtKB/TrEMBL

B4DS98

Related

ENSP00000298119.4, ENST00000298119.9

Conserved Domains (7) summary

cd05764
Location:301 → 374

Ig_2; Subgroup of the immunoglobulin (Ig) superfamily

smart00082
Location:240 → 272

LRRCT; Leucine rich repeat C-terminal domain

cd00116
Location:41 → 207

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 ...

pfam07679
Location:287 → 374

I-set; Immunoglobulin I-set domain

sd00033
Location:53 → 76

LRR_RI; leucine-rich repeat [structural motif]

pfam00041
Location:421 → 494

fn3; Fibronectin type III domain

pfam13855
Location:99 → 159

LRR_8; Leucine rich repeat

RNA

NR_144388.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses a different splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL109662, AL121821, AL138498, AW013887
NR_144389.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL109662, AL121821, AL138498, AW013887

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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

41606876..41904549

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047431029.1 → XP_047286985.1 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

UniProtKB/Swiss-Prot

B3KU78, Q86XL2, Q96NI6

RNA

XR_007063991.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

35797646..36095321

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054375487.1 → XP_054231462.1 leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

UniProtKB/Swiss-Prot

B3KU78, Q86XL2, Q96NI6