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LETM1 leucine zipper and EF-hand containing transmembrane protein 1 [ Homo sapiens (human) ]

Gene ID: 3954, updated on 5-Jan-2025

Summary

Official Symbol
LETM1provided by HGNC
Official Full Name
leucine zipper and EF-hand containing transmembrane protein 1provided by HGNC
Primary source
HGNC:HGNC:6556
See related
Ensembl:ENSG00000168924 MIM:604407; AllianceGenome:HGNC:6556
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KHE; Mdm38; CONDMIM; SLC55A1
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 Wolf-Hirschhorn syndrome, a complex malformation syndrome caused by the deletion of parts of the distal short arm of chromosome 4. Related pseudogenes have been identified on chromosomes 8, 15 and 19. [provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in colon (RPKM 12.1), kidney (RPKM 9.6) and 25 other tissues See more
Orthologs
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Genomic context

See LETM1 in Genome Data Viewer
Location:
4p16.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1811479..1856156, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1809954..1854630, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1813206..1857883, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900648 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1779273-1780036 Neighboring gene CRISPRi-validated cis-regulatory element chr4.260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1796986-1797514 Neighboring gene fibroblast growth factor receptor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1828066-1828868 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1844335-1844585 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1856349-1856525 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:1857091-1857592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1858969-1859764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:1872049-1872550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15151 Neighboring gene RNA, 7SL, cytoplasmic 671, pseudogene Neighboring gene nuclear receptor binding SET domain protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21162 Neighboring gene small Cajal body-specific RNA 22

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-02-03)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2012-02-03)

ClinGen Genome Curation Page

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding PubMed 
enables calcium:proton antiporter activity  
enables calcium:proton antiporter activity PubMed 
enables protein binding PubMed 
enables ribosome binding  
Process Evidence Code Pubs
involved_in calcium export from the mitochondrion PubMed 
involved_in calcium export from the mitochondrion PubMed 
involved_in calcium ion transport PubMed 
involved_in cristae formation PubMed 
involved_in inner mitochondrial membrane organization PubMed 
involved_in mitochondrial calcium ion homeostasis PubMed 
involved_in mitochondrial calcium ion transmembrane transport  
involved_in mitochondrial calcium ion transmembrane transport PubMed 
involved_in mitochondrial calcium ion transmembrane transport PubMed 
involved_in mitochondrial potassium ion transmembrane transport PubMed 
involved_in mitochondrion organization  
involved_in negative regulation of mitochondrial calcium ion concentration PubMed 
involved_in protein hexamerization  
involved_in protein homooligomerization  
involved_in proton transmembrane transport  
involved_in regulation of cellular hyperosmotic salinity response PubMed 
Component Evidence Code Pubs
located_in mitochondrial inner membrane PubMed 
located_in mitochondrion PubMed 
is_active_in mitochondrion  
located_in mitochondrion  
located_in mitochondrion PubMed 

General protein information

Preferred Names
mitochondrial proton/calcium exchanger protein
Names
LETM1 and EF-hand domain-containing protein 1, mitochondrial
Mdm38 homolog
electroneutral mitochondrial K(+)/H(+)exchanger
leucine zipper-EF-hand containing transmembrane protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013063.1 RefSeqGene

    Range
    5092..49769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_012318.3NP_036450.1  mitochondrial proton/calcium exchanger protein precursor

    See identical proteins and their annotated locations for NP_036450.1

    Status: REVIEWED

    Source sequence(s)
    AC105448, AF061025
    Consensus CDS
    CCDS3355.1
    UniProtKB/Swiss-Prot
    B4DED2, O95202, Q9UF65
    Related
    ENSP00000305653.2, ENST00000302787.3
    Conserved Domains (1) summary
    pfam07766
    Location:155410
    LETM1; LETM1-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    1811479..1856156 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713884.2XP_006713947.1  mitochondrial proton/calcium exchanger protein isoform X1

    Conserved Domains (1) summary
    pfam07766
    Location:155410
    LETM1; LETM1-like protein
  2. XM_047415673.1XP_047271629.1  mitochondrial proton/calcium exchanger protein isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    1809954..1854630 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349978.1XP_054205953.1  mitochondrial proton/calcium exchanger protein isoform X1

  2. XM_054349980.1XP_054205955.1  mitochondrial proton/calcium exchanger protein isoform X2

  3. XM_054349979.1XP_054205954.1  mitochondrial proton/calcium exchanger protein isoform X3

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