LRFN1

leucine rich repeat and fibronectin type III domain containing 1, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 19:39306566-39320863

Links

ENSG00000128011 ∙ NCBI:57622 ∙ OMIM:612807 ∙ HGNC:29290 ∙ Uniprot:Q9P244 ∙ 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 LRFN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRFN1 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		1	30			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	30	0	0

Variants in LRFN1

This is a list of pathogenic ClinVar variants found in the LRFN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39307679-C-A		not specified	Uncertain significance (Oct 13, 2021)
19-39307745-A-G		not specified	Uncertain significance (Oct 29, 2021)
19-39307769-T-C		not specified	Uncertain significance (Sep 13, 2023)
19-39307871-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-39307901-G-A		not specified	Uncertain significance (May 23, 2023)
19-39307935-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-39307944-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-39308077-C-A		not specified	Uncertain significance (Oct 06, 2022)
19-39308081-G-C		not specified	Uncertain significance (Mar 28, 2024)
19-39308102-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-39308222-A-G		not specified	Likely benign (May 01, 2024)
19-39308241-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-39308304-G-T		not specified	Uncertain significance (Sep 06, 2022)
19-39308384-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-39308450-C-A		not specified	Uncertain significance (Mar 21, 2024)
19-39308452-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-39308539-C-G		not specified	Uncertain significance (Aug 10, 2023)
19-39313946-T-C		not specified	Uncertain significance (May 18, 2023)
19-39314057-C-G		not specified	Uncertain significance (Dec 05, 2022)
19-39314099-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-39314156-G-A		not specified	Uncertain significance (Nov 08, 2021)
19-39314285-C-G		not specified	Uncertain significance (May 24, 2023)
19-39314291-A-C		not specified	Uncertain significance (Dec 07, 2021)
19-39314423-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-39314592-A-G		not specified	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRFN1	protein_coding	protein_coding	ENST00000248668	2	8769

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.903	0.0972	123735	0	4	123739	0.0000162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.31	305	516	0.591	0.0000373	4773
Missense in Polyphen		96	208	0.46154		1899
Synonymous	2.90	203	263	0.773	0.0000210	1806
Loss of Function	3.29	2	16.3	0.122	8.78e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000849	0.0000653
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000568	0.0000558
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000178
Middle Eastern	0.0000568	0.0000558
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite outgrowth in hippocampal neurons. Involved in the regulation and maintenance of excitatory synapses. Induces the clustering of excitatory postsynaptic proteins, including DLG4, DLGAP1, GRIA1 and GRIN1 (By similarity). {ECO:0000250}.
• Pathway: Neuronal System;Synaptic adhesion-like molecules;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.486
• hipred: Y
• hipred_score: 0.789
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrfn1

Gene ontology

• Biological process: regulation of postsynaptic density assembly
• Cellular component: plasma membrane;cell surface;cell junction;integral component of postsynaptic density membrane