ELFN2 extracellular leucine rich repeat and fibronectin type III domain containing 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ELFN2provided by HGNC
Official Full Name: extracellular leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
Primary source: HGNC:HGNC:29396
See related: Ensembl:ENSG00000166897 MIM:620223; AllianceGenome:HGNC:29396
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: LRRC62; PPP1R29
Summary: Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synaptic membrane adhesion. Predicted to act upstream of or within chemical synaptic transmission; establishment of protein localization; and gene expression. Located in extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in brain (RPKM 10.0) and testis (RPKM 1.9) See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (37340644..37427479, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (37801164..37887955, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (37736685..37823514, complement)

Chromosome 22 - NC_000022.11 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?

Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
Title: Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
Authors conclude that extracellular transsynaptic scaffolding by ELFN2 in the brain is a cardinal organizational feature of group III mGluRs essential for their signaling properties and brain function.
Title: ELFN2 is a postsynaptic cell adhesion molecule with essential roles in controlling group III mGluRs in the brain and neuropsychiatric behavior.

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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
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. 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)

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 ELFN2	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G17846 (e-PCR)
- UniSTS:46460

D22S624 (e-PCR)
- UniSTS:48785

AL008661 (e-PCR)
- UniSTS:7080

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein phosphatase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in synaptic membrane adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein phosphatase 1 regulatory subunit 29

Names: dJ63G5.3 (putative Leucine rich protein); leucine-rich repeat and fibronectin type-III domain-containing protein 6; leucine-rich repeat-containing protein 62

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_052906.5 → NP_443138.2 protein phosphatase 1 regulatory subunit 29 precursor

See identical proteins and their annotated locations for NP_443138.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer trancript and encodes the protein.

Source sequence(s)

AB067491, BC032082, DA398675, FP325335, Z94160

Consensus CDS

CCDS33642.1

UniProtKB/Swiss-Prot

Q5R3F8, Q96PY3

Related

ENSP00000385277.1, ENST00000402918.7

Conserved Domains (4) summary

TIGR00864
Location:157 → 227

PCC; polycystin cation channel protein

sd00031
Location:60 → 80

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:200 → 226

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:80 → 139

LRR_8; Leucine rich repeat

RNA

NR_110512.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two exons and contains two alternate 3' terminal exons, compared to variant 1. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.

Source sequence(s)

DA365834, DA398675, FP325335, Z94160