Gene Gene information from NCBI Gene database.
Entrez ID 3954
Gene name Leucine zipper and EF-hand containing transmembrane protein 1
Gene symbol LETM1
Synonyms (NCBI Gene)
CONDMIMKHEMdm38SLC55A1
Chromosome 4
Chromosome location 4p16.3
Summary This gene encodes a protein that is localized to the inner mitochondrial membrane. The protein functions to maintain the mitochondrial tubular shapes and is required for normal mitochondrial morphology and cellular viability. Mutations in this gene cause
miRNA miRNA information provided by mirtarbase database.
657
miRTarBase ID miRNA Experiments Reference
MIRT016307 hsa-miR-193b-3p Proteomics 21512034
MIRT023539 hsa-miR-1-3p Proteomics 18668040
MIRT028844 hsa-miR-26b-5p Microarray 19088304
MIRT043486 hsa-miR-331-3p CLASH 23622248
MIRT041761 hsa-miR-484 CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
41
GO ID Ontology Definition Evidence Reference
GO:0005509 Function Calcium ion binding IEA
GO:0005509 Function Calcium ion binding TAS 10486213, 26975899
GO:0005515 Function Protein binding IPI 18628306, 25416956, 32296183, 36321428
GO:0005739 Component Mitochondrion HTP 34800366
GO:0005739 Component Mitochondrion IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
604407 6556 ENSG00000168924
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O95202
Protein name Mitochondrial proton/calcium exchanger protein (Electroneutral mitochondrial K(+)/H(+)exchanger) (KHE) (Leucine zipper-EF-hand-containing transmembrane protein 1)
Protein function Plays an important role in maintenance of mitochondrial morphology and in mediating either calcium or potassium/proton antiport (PubMed:18628306, PubMed:19797662, PubMed:24344246, PubMed:24898248, PubMed:29123128, PubMed:32139798, PubMed:3605521
PDB 9BA1
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF07766 LETM1 153 418 LETM1-like protein Family
Sequence
MASILLRSCRGRAPARLPPPPRYTVPRGSPGDPAHLSCASTLGLRNCLNVPFGCCTPIHP
VYTSSRGDHLGCWALRPECLRIVSRAPWTSTSVGFVAVGPQCLPVRGWHSSRPVRDDSVV
EKSLKSLKDKNKKLEEGGPVYSPPAEVVVKKSLGQRVLDELKHYYHGFRLLWIDTKIAAR
MLWRILNGHSLTRRERRQFLRICADLFRLVPFLVFVVVPFMEFLLPVAVKLFPNMLPSTF
ETQSLKEERLKKELRVKLELAKFLQDTIEEMALKNKAAKGSATKDFSVFFQKIRETGERP
SNEEIMRFSKLFEDELTLDNLTRPQLVALCKLLELQSIGTNNFLRFQLTMRLRSIKADDK
LIAEEGVDSLNVKELQAACRARGMRALGVTEDRLRGQLKQWLDLHLHQEIPTSLLILS
RA
MYLPDTLSPADQLKSTLQTLPEIVAKEAQVKVAEVEGEQVDNKAKLEATLQEEAAIQQEH
REKELQKRSEVAKDFEPERVVAAPQRPGTEPQPEMPDTVLQSETLKDTAPVLEGLKEEEI
TKEEIDILSDACSKLQEQKKSLTKEKEELELLKEDVQDYSEDLQEIKKELSKTGEEKYVE
ESKASKRLTKRVQQMIGQIDGLISQLEMDQQAGKLAPANGMPTGENVISVAELINAMKQV
KHIPESKLTSLAAALDENKDGKVNIDDLVKVIELVDKEDVHISTSQVAEIVATLEKEEKV
EEKEKAKEKAEKEVAEVKS
Sequence length 739
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
18
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
LETM1-associated clinical spectrum with predominant nervous system involvement Pathogenic; Likely pathogenic rs2108846420, rs2108846393, rs2108832976, rs2108847729, rs750286012, rs2108846252, rs2108840447, rs753284434 RCV002221675
RCV002221676
RCV002221677
RCV002221679
RCV002221680
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction Pathogenic rs2108846420, rs2108832976, rs750286012, rs753284434 RCV002294478
RCV002294479
RCV002294481
RCV002294482
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
4p partial monosomy syndrome Benign; Likely benign; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Absence of septum pellucidum Absence Of Septum Pellucidum HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer BEFREE 31101574
★☆☆☆☆
Found in Text Mining only
Agenesis of corpus callosum Agenesis Of Corpus Callosum HPO_DG
★☆☆☆☆
Found in Text Mining only
Aplasia cutis congenita of scalp Aplasia Cutis Congenita HPO_DG
★☆☆☆☆
Found in Text Mining only
Arachnodactyly Arachnodactyly HPO_DG
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only
Bladder Neoplasm Bladder Neoplasm BEFREE 29048663
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Brain Diseases Metabolic Brain disease Pubtator 36055214 Associate
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 26722481 Associate
★☆☆☆☆
Found in Text Mining only