LRRN2

leucine rich repeat neuronal 2, the group of I-set domain containing

Basic information

Region (hg38): 1:204617170-204685738

Previous symbols: [ "LRRN5" ]

Links

ENSG00000170382 ∙ NCBI:10446 ∙ OMIM:605492 ∙ HGNC:16914 ∙ Uniprot:O75325 ∙ 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 LRRN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRN2 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	2	3
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	2

Variants in LRRN2

This is a list of pathogenic ClinVar variants found in the LRRN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-204618045-G-C		not specified	Uncertain significance (Aug 30, 2021)
1-204618053-G-A		not specified	Uncertain significance (Nov 28, 2023)
1-204618065-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-204618078-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-204618081-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-204618104-C-A		not specified	Uncertain significance (Mar 18, 2024)
1-204618111-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-204618297-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-204618315-T-C		not specified	Uncertain significance (May 03, 2023)
1-204618348-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-204618353-G-A		not specified	Uncertain significance (May 17, 2023)
1-204618378-A-G		not specified	Uncertain significance (Jan 29, 2024)
1-204618398-C-T		not specified	Uncertain significance (Jun 13, 2024)
1-204618399-G-A		not specified	Uncertain significance (Jan 07, 2022)
1-204618569-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-204618633-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-204618702-G-C		not specified	Uncertain significance (May 10, 2022)
1-204618713-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-204618752-C-T		not specified	Uncertain significance (May 04, 2022)
1-204618767-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-204618768-G-A		not specified	Uncertain significance (May 23, 2023)
1-204618799-C-T			Likely benign (Feb 01, 2023)
1-204618845-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-204618999-G-T		not specified	Uncertain significance (Aug 30, 2022)
1-204619092-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRN2	protein_coding	protein_coding	ENST00000367175	1	68564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.780	0.219	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	333	445	0.748	0.0000287	4541
Missense in Polyphen		111	182.86	0.60702		1965
Synonymous	0.680	181	193	0.938	0.0000112	1622
Loss of Function	3.30	3	18.2	0.165	0.00000104	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.111
• rvis_EVS: -0.28
• rvis_percentile_EVS: 33.53

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.809
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrn2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;signal transduction
• Cellular component: extracellular space;integral component of membrane;extracellular matrix
• Molecular function: signaling receptor activity