LRTM1

leucine rich repeats and transmembrane domains 1

Basic information

Region (hg38): 3:54918231-54967088

Links

ENSG00000144771 ∙ NCBI:57408 ∙ ∙ HGNC:25023 ∙ Uniprot:Q9HBL6 ∙ 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 LRTM1 gene.

• not_specified (44 variants)
• not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRTM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020678.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			41	3	3	47
nonsense					1	1
start loss						0
frameshift				2		2
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	5	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRTM1	protein_coding	protein_coding	ENST00000273286	3	48852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.37e-16	0.000745	125233	2	512	125747	0.00205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.837	221	189	1.17	0.00000974	2228
Missense in Polyphen		74	63.846	1.159		777
Synonymous	-0.840	92	82.3	1.12	0.00000495	717
Loss of Function	-1.57	20	13.7	1.46	8.02e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000914	0.000914
Ashkenazi Jewish	0.0111	0.0112
East Asian	0.00703	0.00698
Finnish	0.000462	0.000462
European (Non-Finnish)	0.00119	0.00119
Middle Eastern	0.00703	0.00698
South Asian	0.00297	0.00294
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0771

Intolerance Scores

• loftool: 0.791
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.99

Haploinsufficiency Scores

• pHI: 0.290
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0431

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrtm1

Gene ontology

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