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

Summary

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; postsynaptic density membrane; and presynaptic active zone membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in brain (RPKM 2.1), spleen (RPKM 1.1) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (39306566..39320863, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (42110835..42125134, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (39797206..39811503, complement)

Chromosome 19 - NC_000019.10 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: 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?

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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU048745 (e-PCR)
- UniSTS:145195

G31081 (e-PCR)
- UniSTS:75584

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
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

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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

39306566..39320863 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NW_025791808.1 Reference GRCh38.p14 PATCHES

Range

86948..101245 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060943.1 Alternate T2T-CHM13v2.0

Range

42110835..42125134 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q8TBS9, Q9P244