LRRTM1

leucine rich repeat transmembrane neuronal 1

Basic information

Region (hg38): 2:80288351-80304752

Links

ENSG00000162951 ∙ NCBI:347730 ∙ OMIM:610867 ∙ HGNC:19408 ∙ Uniprot:Q86UE6 ∙ 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 LRRTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRTM1 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		1
missense			28	1	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	2

Variants in LRRTM1

This is a list of pathogenic ClinVar variants found in the LRRTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-80302418-G-A		not specified	Uncertain significance (Oct 27, 2022)
2-80302444-T-C		not specified	Uncertain significance (Apr 18, 2023)
2-80302463-A-G		not specified	Uncertain significance (Sep 14, 2022)
2-80302478-C-G		not specified	Uncertain significance (Dec 20, 2023)
2-80302520-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-80302530-C-T			Likely benign (May 01, 2023)
2-80302548-C-G		not specified	Uncertain significance (Sep 20, 2023)
2-80302571-C-T		not specified	Uncertain significance (Feb 27, 2023)
2-80302595-C-T		not specified	Uncertain significance (May 04, 2023)
2-80302610-C-G		not specified	Uncertain significance (Apr 08, 2022)
2-80302613-C-A			Benign (May 01, 2024)
2-80302621-C-G		not specified	Uncertain significance (May 05, 2023)
2-80302637-C-T		not specified	Uncertain significance (Apr 20, 2024)
2-80302664-G-T		not specified	Uncertain significance (Aug 30, 2022)
2-80302716-C-G		not specified	Uncertain significance (Jun 23, 2021)
2-80302728-C-G		not specified	Uncertain significance (Mar 24, 2023)
2-80302759-A-T		not specified	Uncertain significance (Jan 17, 2024)
2-80302772-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-80302798-T-C		not specified	Uncertain significance (Dec 08, 2023)
2-80302808-C-T			Benign (Apr 03, 2018)
2-80302817-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-80302843-G-A		not specified	Uncertain significance (Apr 14, 2022)
2-80302877-G-C		not specified	Uncertain significance (Dec 22, 2023)
2-80302955-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-80303026-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRTM1	protein_coding	protein_coding	ENST00000295057	1	16392

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.595	0.405	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	230	299	0.769	0.0000141	3390
Missense in Polyphen		83	135.02	0.61473		1658
Synonymous	-0.466	149	142	1.05	0.00000711	1090
Loss of Function	2.98	3	15.8	0.190	6.91e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation, acting at both pre- and postsynaptic level. {ECO:0000250}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.138
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.597
• hipred: Y
• hipred_score: 0.837
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrtm1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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)

Gene ontology

• Biological process: negative regulation of receptor internalization;locomotory behavior;biological_process;protein localization to synapse;exploration behavior;synapse organization;positive regulation of synapse assembly;long-term synaptic potentiation;regulation of postsynaptic density assembly;regulation of presynapse assembly
• Cellular component: extracellular space;endoplasmic reticulum;cell surface;cell junction;axon;growth cone;extracellular matrix;excitatory synapse;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic specialization membrane
• Molecular function: molecular_function