LRTM1

leucine rich repeats and transmembrane domains 1

Basic information

Region (hg38): 3:54918231-54967088

Links

ENSG00000144771NCBI:57408HGNC:25023Uniprot:Q9HBL6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRTM1 gene.

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.

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
15
clinvar
1
clinvar
3
clinvar
19
nonsense
1
clinvar
1
start loss
0
frameshift
2
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 3 4

Variants in LRTM1

This is a list of pathogenic ClinVar variants found in the LRTM1 region.

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

Position Type Phenotype Significance ClinVar
3-54918478-A-G not specified Uncertain significance (Apr 22, 2024)3292120
3-54918482-GCT-G Likely benign (Jan 01, 2023)767916
3-54918580-G-A not specified Uncertain significance (Nov 13, 2023)3121242
3-54918617-C-T Benign (May 24, 2018)784010
3-54918625-A-G not specified Uncertain significance (Jun 21, 2021)2203843
3-54918638-C-A not specified Uncertain significance (Jan 31, 2022)3121241
3-54918649-C-T not specified Uncertain significance (Feb 17, 2023)2459749
3-54918661-G-A not specified Uncertain significance (Oct 05, 2023)3121240
3-54918700-C-A Benign (Dec 31, 2019)791931
3-54918704-C-G Benign (Dec 31, 2019)709209
3-54918709-G-A not specified Uncertain significance (Feb 07, 2023)3121239
3-54918758-G-A not specified Uncertain significance (May 20, 2024)3292122
3-54918837-G-T not specified Uncertain significance (Apr 09, 2024)3292123
3-54918872-T-C not specified Uncertain significance (Dec 18, 2023)3121238
3-54918874-A-G not specified Uncertain significance (May 21, 2024)3292126
3-54924640-G-C not specified Uncertain significance (Jul 19, 2022)2374178
3-54924732-G-A not specified Uncertain significance (Dec 14, 2021)2266738
3-54924732-G-T not specified Uncertain significance (Apr 26, 2024)3292121
3-54924735-C-T not specified Uncertain significance (Oct 05, 2023)3121237
3-54924736-G-A Benign (Dec 31, 2019)738018
3-54924741-A-G not specified Uncertain significance (Sep 14, 2023)2624282
3-54924775-T-C not specified Likely benign (Jun 16, 2023)2591971
3-54924844-G-A not specified Uncertain significance (Apr 11, 2023)2514172
3-54924846-T-C not specified Uncertain significance (Mar 30, 2022)2280941
3-54924975-T-A not specified Uncertain significance (Sep 08, 2023)2620869

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LRTM1protein_codingprotein_codingENST00000273286 348852
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.37e-160.00074512523325121257470.00205
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.8372211891.170.000009742228
Missense in Polyphen7463.8461.159777
Synonymous-0.8409282.31.120.00000495717
Loss of Function-1.572013.71.468.02e-7137

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009140.000914
Ashkenazi Jewish0.01110.0112
East Asian0.007030.00698
Finnish0.0004620.000462
European (Non-Finnish)0.001190.00119
Middle Eastern0.007030.00698
South Asian0.002970.00294
Other0.001960.00196

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lrtm1
Phenotype

Gene ontology

Biological process
positive regulation of synapse assembly
Cellular component
integral component of membrane
Molecular function