LRRTM2

leucine rich repeat transmembrane neuronal 2

Basic information

Region (hg38): 5:138868921-138875368

Links

ENSG00000146006

∙ NCBI:26045 ∙ OMIM:610868 ∙ HGNC:19409 ∙ Uniprot:O43300 ∙ 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 LRRTM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRTM2 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			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in LRRTM2

This is a list of pathogenic ClinVar variants found in the LRRTM2 region.

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

Position	Phenotype	Significance	ClinVar
5-138869248-T-C	Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)	223765
5-138873093-T-G	not specified	Uncertain significance (Dec 27, 2023)	3121216
5-138873096-G-T	not specified	Uncertain significance (Mar 20, 2023)	2526777
5-138873149-G-A	not specified	Uncertain significance (Dec 01, 2022)	2371087
5-138873347-A-G	not specified	Uncertain significance (May 17, 2023)	2548191
5-138873403-G-T	not specified	Uncertain significance (Dec 27, 2023)	3121215
5-138873425-G-A	not specified	Uncertain significance (Aug 04, 2023)	2616062
5-138873449-G-A	not specified	Uncertain significance (Nov 21, 2022)	2329191
5-138873539-C-T	not specified	Uncertain significance (Jun 04, 2024)	3292110
5-138873601-A-C	not specified	Uncertain significance (Sep 22, 2023)	3121219
5-138873611-G-A	not specified	Uncertain significance (Dec 16, 2022)	2341171
5-138873656-G-T	not specified	Uncertain significance (May 23, 2023)	2524022
5-138873863-G-A	not specified	Uncertain significance (Jul 30, 2023)	2592508
5-138874020-G-A	not specified	Uncertain significance (Jul 20, 2021)	2239008
5-138874041-C-T	not specified	Uncertain significance (Feb 06, 2023)	2480913
5-138874124-G-A	not specified	Uncertain significance (Feb 28, 2024)	3121218
5-138874307-C-G	not specified	Uncertain significance (Oct 26, 2022)	2211962
5-138874383-C-T	not specified	Uncertain significance (Feb 14, 2024)	3121217
5-138874890-A-C	Hereditary cancer-predisposing syndrome	Likely benign (Dec 01, 2015)	223788

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRTM2	protein_coding	protein_coding	ENST00000274711	2	6446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.809	0.191	124633	0	4	124637	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	190	279	0.682	0.0000152	3387
Missense in Polyphen		55	112.31	0.48969		1428
Synonymous	0.942	97	110	0.886	0.00000598	1022
Loss of Function	3.36	3	18.6	0.161	0.00000115	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the development and maintenance of excitatory synapse in the vertebrate nervous system. Regulates surface expression of AMPA receptors and instructs the development of functional glutamate release sites. Acts as a ligand for the presynaptic receptors NRXN1-A and NRXN1-B (By similarity). {ECO:0000250}.;
Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

pRec: 0.118

Intolerance Scores

loftool: 0.246
rvis_EVS: -0.6
rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

pHI: 0.817
hipred: Y
hipred_score: 0.768
ghis: 0.416

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lrrtm2
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;synapse organization;positive regulation of synapse assembly;long-term synaptic potentiation;regulation of postsynaptic density assembly
Cellular component: cell junction;excitatory synapse;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic specialization membrane;integral component of postsynaptic density membrane
Molecular function: neurexin family protein binding