LRRN3

leucine rich repeat neuronal 3, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 7:111091005-111125454

Links

ENSG00000173114 ∙ NCBI:54674 ∙ OMIM:619748 ∙ HGNC:17200 ∙ Uniprot:Q9H3W5 ∙ 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 LRRN3 gene.

• Inborn genetic diseases (23 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRN3 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					3	3
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	4

Variants in LRRN3

This is a list of pathogenic ClinVar variants found in the LRRN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-111122779-G-T		not specified	Uncertain significance (Sep 27, 2021)
7-111122785-C-A		not specified	Uncertain significance (Oct 03, 2022)
7-111122863-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-111122864-G-A			Benign (Feb 07, 2018)
7-111123037-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-111123100-A-G		not specified	Uncertain significance (Sep 07, 2022)
7-111123248-C-G		not specified	Uncertain significance (Feb 27, 2023)
7-111123447-A-G			Benign (Oct 09, 2017)
7-111123463-G-A		not specified	Uncertain significance (Nov 17, 2023)
7-111123553-A-C		not specified	Uncertain significance (Jun 22, 2023)
7-111123599-G-A		not specified	Uncertain significance (Feb 03, 2022)
7-111123634-G-C		not specified	Uncertain significance (Oct 12, 2022)
7-111123672-C-T			Benign (Oct 09, 2017)
7-111123833-T-C		not specified	Uncertain significance (Jan 30, 2024)
7-111123862-A-G		not specified	Uncertain significance (May 17, 2023)
7-111123903-T-C			Benign (Oct 09, 2017)
7-111123971-C-A		not specified	Uncertain significance (May 09, 2022)
7-111123994-C-T		not specified	Uncertain significance (Sep 20, 2023)
7-111124000-G-A		not specified	Uncertain significance (Nov 03, 2023)
7-111124015-A-G		not specified	Uncertain significance (Jul 14, 2023)
7-111124076-A-C		not specified	Uncertain significance (Jun 12, 2023)
7-111124130-A-T		not specified	Uncertain significance (Dec 13, 2022)
7-111124256-C-T		not specified	Uncertain significance (Jan 24, 2023)
7-111124282-G-A		not specified	Uncertain significance (Dec 28, 2022)
7-111124301-T-C		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRN3	protein_coding	protein_coding	ENST00000451085	1	34449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0324	0.966	125671	0	23	125694	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	311	367	0.847	0.0000175	4676
Missense in Polyphen		98	145.66	0.67282		1910
Synonymous	0.533	126	134	0.941	0.00000650	1404
Loss of Function	2.75	6	18.9	0.317	0.00000118	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000601	0.000601
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.468
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.595
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.623

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrn3
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of synapse assembly
• Cellular component: integral component of membrane