LRFN4

leucine rich repeat and fibronectin type III domain containing 4, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 11:66856647-66860475

Links

ENSG00000173621 ∙ NCBI:78999 ∙ OMIM:612810 ∙ HGNC:28456 ∙ Uniprot:Q6PJG9 ∙ 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 LRFN4 gene.

• Pyruvate carboxylase deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRFN4 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				1		1
missense			39			39
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	39	1	0

Highest pathogenic variant AF is 0.0000263

Variants in LRFN4

This is a list of pathogenic ClinVar variants found in the LRFN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66858057-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-66858090-C-T		not specified	Uncertain significance (Mar 16, 2024)
11-66858253-C-T		not specified	Uncertain significance (Jan 29, 2024)
11-66858297-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-66858312-G-A		not specified	Uncertain significance (May 31, 2023)
11-66858373-C-T		not specified	Uncertain significance (Oct 06, 2022)
11-66858388-C-T		not specified	Uncertain significance (Nov 15, 2023)
11-66858390-C-A		not specified	Uncertain significance (Jun 01, 2023)
11-66858396-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-66858408-G-A		not specified	Uncertain significance (Nov 27, 2023)
11-66858484-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-66858489-G-C		not specified	Uncertain significance (May 02, 2024)
11-66858490-C-T		not specified	Uncertain significance (Dec 16, 2021)
11-66858540-C-T		not specified	Uncertain significance (May 21, 2024)
11-66858560-C-T			Likely benign (Jul 01, 2022)
11-66858567-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-66858663-G-C		not specified	Uncertain significance (Dec 14, 2023)
11-66858777-G-A		not specified	Uncertain significance (Mar 30, 2022)
11-66858904-C-T		not specified	Uncertain significance (May 05, 2023)
11-66858915-G-A		not specified	Uncertain significance (Feb 01, 2023)
11-66858921-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-66858924-C-T		not specified	Uncertain significance (Jan 18, 2022)
11-66858944-G-T		not specified	Uncertain significance (Apr 06, 2024)
11-66858990-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-66859020-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRFN4	protein_coding	protein_coding	ENST00000309602	2	3829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.913	0.0869	125348	0	9	125357	0.0000359

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	347	419	0.828	0.0000305	3893
Missense in Polyphen		102	158.2	0.64477		1669
Synonymous	-0.928	220	203	1.08	0.0000155	1500
Loss of Function	2.98	1	12.2	0.0816	6.81e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000323	0.0000323
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000562	0.0000530
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000409	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite outgrowth in hippocampal neurons. 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: 0.112

Haploinsufficiency Scores

• pHI: 0.300
• hipred: Y
• hipred_score: 0.662
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrfn4
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of postsynaptic density assembly;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: plasma membrane;cell surface;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding