LRRTM3

leucine rich repeat transmembrane neuronal 3

Basic information

Region (hg38): 10:66926036-67101551

Links

ENSG00000198739 ∙ NCBI:347731 ∙ OMIM:610869 ∙ HGNC:19410 ∙ Uniprot:Q86VH5 ∙ 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 LRRTM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRTM3 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in LRRTM3

This is a list of pathogenic ClinVar variants found in the LRRTM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-66926939-T-C		not specified	Uncertain significance (Oct 02, 2023)
10-66927082-C-A		not specified	Uncertain significance (Feb 23, 2023)
10-66927227-C-T		Arrhythmogenic right ventricular dysplasia 13	Uncertain significance (May 28, 2019)
10-66927299-C-T		not specified	Uncertain significance (Apr 13, 2022)
10-66927352-C-T		not specified	Uncertain significance (Apr 13, 2022)
10-66927576-C-T			Likely benign (Jul 01, 2024)
10-66927584-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-66927761-G-T		not specified	Uncertain significance (Dec 17, 2021)
10-66928030-G-T		not specified	Uncertain significance (May 01, 2024)
10-66928094-C-T		not specified	Uncertain significance (Aug 01, 2022)
10-66928097-C-T		not specified	Uncertain significance (Mar 19, 2024)
10-66928103-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-66928105-C-A		not specified	Uncertain significance (Oct 20, 2023)
10-66928117-G-T		not specified	Uncertain significance (Feb 01, 2023)
10-66928155-G-T		not specified	Uncertain significance (Dec 20, 2023)
10-66928166-T-C		not specified	Uncertain significance (Nov 08, 2022)
10-66928189-G-A		not specified	Uncertain significance (Aug 12, 2022)
10-66928194-G-T			Likely benign (Aug 01, 2024)
10-66928444-G-A		not specified	Uncertain significance (Sep 14, 2023)
10-67097690-C-T		not specified	Uncertain significance (Jun 17, 2024)
10-67097708-C-T		not specified	Uncertain significance (May 23, 2023)
10-67097719-C-T		not specified	Uncertain significance (Jun 02, 2023)
10-67097765-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRTM3	protein_coding	protein_coding	ENST00000361320	3	173825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0248	125718	0	7	125725	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	219	313	0.701	0.0000162	3808
Missense in Polyphen		61	121.76	0.501		1544
Synonymous	-0.113	129	127	1.01	0.00000633	1164
Loss of Function	3.75	2	20.2	0.0991	0.00000111	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits a limited synaptogenic activity in vitro, restricted to excitatory presynaptic differentiation (By similarity). May play a role in the development and maintenance of the vertebrate nervous system. {ECO:0000250}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.186
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.814
• hipred: Y
• hipred_score: 0.800
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrtm3
• 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); normal phenotype

Gene ontology

• Biological process: positive regulation of synapse assembly;presynapse assembly;positive regulation of amyloid-beta formation
• Cellular component: extracellular space;cell junction;extracellular matrix;glutamatergic synapse;integral component of postsynaptic density membrane