LRRTM4

leucine rich repeat transmembrane neuronal 4

Basic information

Region (hg38): 2:76747685-77593319

Links

ENSG00000176204 ∙ NCBI:80059 ∙ OMIM:610870 ∙ HGNC:19411 ∙ Uniprot:Q86VH4 ∙ 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 LRRTM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRTM4 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			23	1		24
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in LRRTM4

This is a list of pathogenic ClinVar variants found in the LRRTM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-76748741-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-76748774-A-C		not specified	Uncertain significance (Dec 21, 2023)
2-76748805-G-C		not specified	Uncertain significance (Mar 16, 2022)
2-77518322-C-G		not specified	Uncertain significance (Jun 13, 2024)
2-77518380-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-77518425-G-T		not specified	Uncertain significance (Dec 21, 2023)
2-77518500-G-C		not specified	Uncertain significance (May 08, 2023)
2-77518535-A-G		not specified	Uncertain significance (Sep 26, 2022)
2-77518538-T-C		not specified	Uncertain significance (Jul 15, 2021)
2-77518656-A-T		not specified	Uncertain significance (Sep 22, 2023)
2-77518749-C-G		not specified	Uncertain significance (Jan 16, 2024)
2-77518755-G-A		not specified	Uncertain significance (May 20, 2024)
2-77518827-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-77518836-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-77518997-T-C		not specified	Uncertain significance (Oct 13, 2021)
2-77519022-T-C		not specified	Uncertain significance (Dec 15, 2022)
2-77519061-G-A		not specified	Uncertain significance (May 29, 2024)
2-77519099-T-C		not specified	Uncertain significance (Dec 15, 2023)
2-77519119-C-A		not specified	Uncertain significance (Jun 28, 2022)
2-77519349-T-C		not specified	Uncertain significance (Dec 19, 2022)
2-77519452-G-T		not specified	Uncertain significance (Dec 06, 2022)
2-77519453-T-G		not specified	Uncertain significance (Dec 06, 2022)
2-77519463-G-A		LRRTM4-related disorder	Uncertain significance (Sep 26, 2024)
2-77519493-T-C		not specified	Uncertain significance (Mar 17, 2023)
2-77519525-AT-A		not specified	Uncertain significance (Nov 10, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRTM4	protein_coding	protein_coding	ENST00000409093	3	845601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0858	0.914	124629	0	26	124655	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	242	322	0.751	0.0000169	3854
Missense in Polyphen		80	140.24	0.57046		1779
Synonymous	-0.00888	127	127	1.00	0.00000684	1143
Loss of Function	3.12	6	21.7	0.277	0.00000115	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000291	0.000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.0000888	0.0000885
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.438
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.256
• hipred: Y
• hipred_score: 0.743
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.275

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrtm4
• 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

• Cellular component: extracellular space;integral component of membrane;cell junction;extracellular matrix;postsynaptic membrane