LRRN4

leucine rich repeat neuronal 4, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 20:6040546-6054060

Previous symbols: [ "C20orf75" ]

Links

ENSG00000125872 ∙ NCBI:164312 ∙ OMIM:619706 ∙ HGNC:16208 ∙ Uniprot:Q8WUT4 ∙ 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 LRRN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRN4 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				2		2
missense			49	4		53
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	6	0

Variants in LRRN4

This is a list of pathogenic ClinVar variants found in the LRRN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-6041117-G-T		not specified	Uncertain significance (Feb 22, 2023)
20-6041152-G-A		not specified	Uncertain significance (Jan 04, 2022)
20-6041158-G-A		not specified	Likely benign (Sep 20, 2023)
20-6041195-G-A		not specified	Likely benign (May 30, 2023)
20-6041197-A-C		not specified	Uncertain significance (May 18, 2023)
20-6041204-C-T		not specified	Uncertain significance (Apr 21, 2022)
20-6041225-A-G		not specified	Uncertain significance (Dec 04, 2023)
20-6041300-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-6041320-G-C		not specified	Uncertain significance (Feb 16, 2023)
20-6041342-G-T		not specified	Uncertain significance (Apr 27, 2023)
20-6041434-T-C		not specified	Uncertain significance (Aug 29, 2022)
20-6041464-G-T		not specified	Uncertain significance (Jun 17, 2024)
20-6041486-C-G		not specified	Uncertain significance (Nov 01, 2022)
20-6041498-G-A		not specified	Uncertain significance (Mar 11, 2022)
20-6041525-T-A		not specified	Uncertain significance (Jul 12, 2022)
20-6041540-G-A		not specified	Uncertain significance (Jul 09, 2021)
20-6041545-C-T		not specified	Uncertain significance (Jul 11, 2023)
20-6041552-G-A		not specified	Uncertain significance (Mar 01, 2024)
20-6041595-A-T		not specified	Uncertain significance (Jan 24, 2024)
20-6041668-T-G		not specified	Uncertain significance (Jan 09, 2024)
20-6041672-C-A		not specified	Uncertain significance (Oct 20, 2023)
20-6041692-T-G		not specified	Uncertain significance (Jan 03, 2024)
20-6041750-G-T		not specified	Uncertain significance (May 02, 2024)
20-6041808-G-A			Likely benign (Sep 01, 2022)
20-6041870-C-T		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRN4	protein_coding	protein_coding	ENST00000378858	4	13272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-9	0.189	125581	0	167	125748	0.000664

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.989	375	433	0.866	0.0000265	4579
Missense in Polyphen		82	106.24	0.77181		1287
Synonymous	1.10	202	223	0.906	0.0000156	1664
Loss of Function	0.504	15	17.3	0.869	8.29e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.00501	0.00441
Finnish	0.00	0.00
European (Non-Finnish)	0.000296	0.000281
Middle Eastern	0.00501	0.00441
South Asian	0.000559	0.000523
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in hippocampus-dependent long-lasting memory. {ECO:0000250}.

Recessive Scores

• pRec: 0.0964

Haploinsufficiency Scores

• pHI: 0.0775
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.433

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrn4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: long-term memory;visual learning
• Cellular component: integral component of plasma membrane;extracellular exosome