LRRN1

leucine rich repeat neuronal 1, the group of I-set domain containing

Basic information

Region (hg38): 3:3799431-3849834

Links

ENSG00000175928 ∙ NCBI:57633 ∙ OMIM:619623 ∙ HGNC:20980 ∙ Uniprot:Q6UXK5 ∙ 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 LRRN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRN1 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				5	5	10
missense			29	4	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	9	6

Variants in LRRN1

This is a list of pathogenic ClinVar variants found in the LRRN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-3844731-T-C			Likely benign (Jul 16, 2018)
3-3844734-G-C		not specified	Uncertain significance (Jun 09, 2022)
3-3844798-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-3844817-A-G		not specified	Uncertain significance (Nov 19, 2022)
3-3844928-A-C		not specified	Uncertain significance (Dec 20, 2023)
3-3844978-G-C		not specified	Uncertain significance (Jun 11, 2024)
3-3845037-C-T			Benign (Dec 31, 2019)
3-3845092-A-C		not specified	Uncertain significance (Jun 09, 2022)
3-3845100-C-T			Benign (Dec 31, 2019)
3-3845122-C-A		not specified	Likely benign (Dec 08, 2023)
3-3845131-G-T		not specified	Likely benign (Aug 21, 2023)
3-3845212-C-T		not specified	Uncertain significance (Dec 14, 2023)
3-3845230-A-C		not specified	Uncertain significance (Feb 06, 2024)
3-3845264-A-T		not specified	Uncertain significance (Jun 29, 2023)
3-3845404-C-T		not specified	Uncertain significance (May 09, 2024)
3-3845471-A-G		not specified	Uncertain significance (Feb 14, 2023)
3-3845499-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-3845558-A-G		not specified	Uncertain significance (May 18, 2023)
3-3845589-G-C		not specified	Uncertain significance (Apr 20, 2023)
3-3845625-C-T			Likely benign (Mar 01, 2023)
3-3845629-C-G		not specified	Uncertain significance (Jan 30, 2024)
3-3845704-A-G		not specified	Uncertain significance (May 08, 2024)
3-3845731-C-T		not specified	Uncertain significance (Aug 16, 2021)
3-3845793-C-T			Likely benign (Apr 16, 2018)
3-3845801-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRN1	protein_coding	protein_coding	ENST00000319331	1	48267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0300	125712	0	12	125724	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	368	387	0.950	0.0000215	4755
Missense in Polyphen		73	107.27	0.68051		1426
Synonymous	-1.78	181	153	1.18	0.00000909	1390
Loss of Function	3.69	2	19.7	0.102	0.00000101	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.21

Haploinsufficiency Scores

• pHI: 0.609
• hipred: Y
• hipred_score: 0.640
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrn1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: lrrn1
• Affected structure: olfactory bulb glomerulus
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: positive regulation of synapse assembly
• Cellular component: extracellular space;integral component of membrane;extracellular matrix