LETM2

leucine zipper and EF-hand containing transmembrane protein 2, the group of Solute carrier family 55, LETM mitochondrial cation/proton exchangers|EF-hand domain containing

Basic information

Region (hg38): 8:38386206-38409527

Links

ENSG00000165046 ∙ NCBI:137994 ∙ ∙ HGNC:14648 ∙ Uniprot:Q2VYF4 ∙ 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 LETM2 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LETM2 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	17	0	1

Variants in LETM2

This is a list of pathogenic ClinVar variants found in the LETM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-38392669-C-A		not specified	Uncertain significance (Apr 13, 2022)
8-38392703-G-C		not specified	Uncertain significance (May 10, 2023)
8-38392766-C-G		not specified	Uncertain significance (Oct 12, 2021)
8-38392798-G-A		not specified	Uncertain significance (Aug 28, 2023)
8-38392806-C-G		not specified	Uncertain significance (Dec 26, 2023)
8-38392831-A-T		not specified	Uncertain significance (Aug 08, 2022)
8-38392962-T-G		not specified	Uncertain significance (Mar 21, 2023)
8-38394125-C-T		not specified	Uncertain significance (Feb 28, 2023)
8-38394218-A-C		not specified	Uncertain significance (Dec 01, 2022)
8-38394218-A-G		not specified	Uncertain significance (Apr 13, 2022)
8-38400360-G-C		not specified	Uncertain significance (Dec 20, 2023)
8-38400381-C-G		not specified	Uncertain significance (Dec 20, 2021)
8-38400893-G-A		not specified	Uncertain significance (Jan 10, 2022)
8-38400911-A-C		not specified	Uncertain significance (Mar 20, 2023)
8-38401050-T-G		not specified	Uncertain significance (Feb 07, 2023)
8-38402577-C-A		not specified	Uncertain significance (Feb 10, 2022)
8-38402589-G-A		not specified	Uncertain significance (May 27, 2022)
8-38402613-C-T		not specified	Uncertain significance (Dec 01, 2022)
8-38404420-G-A		not specified	Uncertain significance (Nov 02, 2023)
8-38404447-C-T		not specified	Uncertain significance (Jun 23, 2023)
8-38404715-T-C			Benign (Oct 29, 2020)
8-38406965-T-C		not specified	Likely benign (Dec 09, 2023)
8-38406970-G-C		not specified	Uncertain significance (Feb 11, 2022)
8-38407375-T-C		not specified	Uncertain significance (Nov 13, 2023)
8-38407420-C-A		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LETM2	protein_coding	protein_coding	ENST00000523983	9	23321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-18	0.00131	125278	6	464	125748	0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0617	228	225	1.01	0.0000113	2871
Missense in Polyphen		49	46.869	1.0455		668
Synonymous	0.347	84	88.1	0.953	0.00000465	874
Loss of Function	-0.501	26	23.4	1.11	0.00000136	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00468	0.00468
Ashkenazi Jewish	0.00228	0.00228
East Asian	0.00138	0.00136
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000555	0.000545
Middle Eastern	0.00138	0.00136
South Asian	0.00856	0.00840
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0742

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.81

Haploinsufficiency Scores

• pHI: 0.0927
• hipred: N
• hipred_score: 0.167
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Letm2

Gene ontology

• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: ribosome binding