LRFN3

leucine rich repeat and fibronectin type III domain containing 3, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 19:35935358-35946624

Links

ENSG00000126243 ∙ NCBI:79414 ∙ OMIM:612809 ∙ HGNC:28370 ∙ Uniprot:Q9BTN0 ∙ 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 LRFN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRFN3 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						0
missense			49	2		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	2	0

Variants in LRFN3

This is a list of pathogenic ClinVar variants found in the LRFN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35939439-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-35939456-C-G		not specified	Uncertain significance (Jun 16, 2023)
19-35939460-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-35939514-G-A		not specified	Uncertain significance (Jan 12, 2024)
19-35939523-G-A		not specified	Uncertain significance (Jun 30, 2022)
19-35939582-G-A		not specified	Uncertain significance (Jun 07, 2023)
19-35939592-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-35939601-G-A		not specified	Uncertain significance (Jul 17, 2023)
19-35939655-G-A		not specified	Uncertain significance (May 25, 2022)
19-35939670-T-C		not specified	Uncertain significance (Oct 12, 2022)
19-35939675-G-A		not specified	Uncertain significance (Nov 22, 2022)
19-35939717-G-A		not specified	Uncertain significance (May 01, 2024)
19-35939824-G-T		not specified	Uncertain significance (Aug 16, 2021)
19-35939858-G-A		not specified	Uncertain significance (Sep 12, 2023)
19-35939870-G-A		not specified	Likely benign (Oct 03, 2023)
19-35939930-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-35940030-G-A		not specified	Uncertain significance (Feb 17, 2022)
19-35940069-G-A		not specified	Uncertain significance (May 31, 2023)
19-35940116-C-T		not specified	Uncertain significance (Feb 06, 2023)
19-35940129-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-35940140-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-35940251-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-35940299-G-A		not specified	Uncertain significance (May 05, 2022)
19-35940314-G-A		not specified	Uncertain significance (Jul 26, 2022)
19-35940389-G-A		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRFN3	protein_coding	protein_coding	ENST00000588831	2	10410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0267	125608	0	26	125634	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	307	439	0.699	0.0000331	3873
Missense in Polyphen		81	153.06	0.52919		1446
Synonymous	0.192	223	227	0.984	0.0000182	1533
Loss of Function	3.10	0	11.2	0.00	4.79e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000691	0.000645
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000955	0.0000880
Middle Eastern	0.00	0.00
South Asian	0.0000987	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule that mediates homophilic cell- cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons (By similarity). {ECO:0000250}.
• Pathway: Neuronal System;Synaptic adhesion-like molecules;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.186
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.73

Haploinsufficiency Scores

• pHI: 0.239
• hipred: Y
• hipred_score: 0.707
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.390

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrfn3
• 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: regulation of synaptic membrane adhesion;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: plasma membrane;cell surface;cell junction;axon;dendrite;glutamatergic synapse;integral component of presynaptic active zone membrane;integral component of postsynaptic density membrane