LRFN2

leucine rich repeat and fibronectin type III domain containing 2, the group of Ig-like cell adhesion molecule family|Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 6:40391590-40587364

Previous symbols: [ "KIAA1246", "SALM1" ]

Links

ENSG00000156564 ∙ NCBI:57497 ∙ OMIM:612808 ∙ HGNC:21226 ∙ Uniprot:Q9ULH4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRFN2 gene.

• Inborn genetic diseases (33 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRFN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	0

Variants in LRFN2

This is a list of pathogenic ClinVar variants found in the LRFN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-40392077-G-A		not specified	Uncertain significance (Sep 22, 2023)
6-40392096-C-A			Benign/Likely benign (Sep 01, 2022)
6-40392097-G-C		not specified	Uncertain significance (Jul 14, 2023)
6-40392101-C-T		not specified	Uncertain significance (May 09, 2023)
6-40392260-C-G		not specified	Uncertain significance (Aug 02, 2023)
6-40392263-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-40392274-G-A		not specified	Uncertain significance (Feb 03, 2022)
6-40392351-G-C		not specified	Uncertain significance (Nov 30, 2022)
6-40392371-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-40392373-G-C		not specified	Uncertain significance (Aug 01, 2022)
6-40392391-C-T		not specified	Uncertain significance (Aug 21, 2023)
6-40392403-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-40392413-C-A		not specified	Uncertain significance (Jul 26, 2022)
6-40392453-G-C		not specified	Uncertain significance (Dec 26, 2023)
6-40392461-C-A		not specified	Uncertain significance (Feb 16, 2023)
6-40392500-G-A		not specified	Uncertain significance (Aug 11, 2022)
6-40392526-G-A			Likely benign (Sep 01, 2022)
6-40392559-G-A		not specified	Uncertain significance (Dec 20, 2021)
6-40392662-C-T		not specified	Uncertain significance (Jan 02, 2024)
6-40392719-C-T		not specified	Uncertain significance (Feb 10, 2023)
6-40392783-G-A			Likely benign (Sep 01, 2022)
6-40392853-T-C			Uncertain significance (Jan 01, 2024)
6-40431771-C-T		not specified	Uncertain significance (Nov 05, 2021)
6-40431849-G-A		not specified	Uncertain significance (Oct 12, 2022)
6-40431883-C-G		not specified	Uncertain significance (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRFN2	protein_coding	protein_coding	ENST00000338305	2	195880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0137	0.980	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	406	508	0.800	0.0000336	5064
Missense in Polyphen		107	194.72	0.54951		2082
Synonymous	-1.02	252	232	1.09	0.0000162	1755
Loss of Function	2.41	6	16.6	0.362	8.61e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000637	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity). {ECO:0000250}.
• Pathway: Neuronal System;Synaptic adhesion-like molecules;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.299
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.476
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lrfn2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: modulation of chemical synaptic transmission;regulation of postsynapse organization
• Cellular component: plasma membrane;cell surface;integral component of membrane;cell junction;postsynaptic membrane;Schaffer collateral - CA1 synapse