LRTM2

leucine rich repeats and transmembrane domains 2

Basic information

Region (hg38): 12:1820266-1836753

Links

ENSG00000166159 ∙ NCBI:654429 ∙ ∙ HGNC:32443 ∙ Uniprot:Q8N967 ∙ 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 LRTM2 gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRTM2 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			16	2		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	16	3	0

Variants in LRTM2

This is a list of pathogenic ClinVar variants found in the LRTM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-1828174-G-A		not specified	Likely benign (Aug 02, 2022)
12-1828192-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-1828200-T-C		not specified	Uncertain significance (Jan 26, 2022)
12-1830973-C-T		not specified	Uncertain significance (Sep 28, 2021)
12-1831033-G-A		not specified	Uncertain significance (Jan 18, 2022)
12-1831063-G-A		not specified	Uncertain significance (May 30, 2023)
12-1831109-G-C		not specified	Uncertain significance (May 04, 2023)
12-1831132-G-A		not specified	Uncertain significance (Aug 03, 2022)
12-1831136-A-C		not specified	Uncertain significance (Sep 13, 2023)
12-1831154-G-A		not specified	Uncertain significance (Nov 03, 2023)
12-1831216-A-G		not specified	Uncertain significance (Aug 01, 2022)
12-1831263-C-A		not specified	Uncertain significance (Dec 01, 2022)
12-1831269-C-A		not specified	Uncertain significance (Mar 07, 2024)
12-1831276-C-T		not specified	Uncertain significance (Sep 29, 2023)
12-1831312-A-C		not specified	Uncertain significance (Jun 06, 2022)
12-1831318-G-A		not specified	Uncertain significance (Nov 10, 2023)
12-1831351-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-1831358-T-C		not specified	Likely benign (Jan 31, 2022)
12-1831376-C-G		not specified	Uncertain significance (Dec 18, 2023)
12-1831409-G-A		not specified	Uncertain significance (Jun 12, 2023)
12-1834452-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-1834506-C-T		not specified	Uncertain significance (Mar 23, 2023)
12-1834511-G-A			Likely benign (Dec 01, 2022)
12-1834513-C-A		not specified	Uncertain significance (Jun 12, 2023)
12-1834689-G-C		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRTM2	protein_coding	protein_coding	ENST00000543818	3	16486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.872	0.128	125042	0	2	125044	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	204	225	0.909	0.0000124	2384
Missense in Polyphen		54	85.191	0.63387		902
Synonymous	-2.24	133	104	1.28	0.00000626	797
Loss of Function	2.81	1	11.1	0.0902	5.31e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000906	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.0667
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.749
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrtm2

Gene ontology

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