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    LETMD1 LETM1 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 25875, updated on 27-Nov-2024

    Summary

    Official Symbol
    LETMD1provided by HGNC
    Official Full Name
    LETM1 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:24241
    See related
    Ensembl:ENSG00000050426 MIM:619070; AllianceGenome:HGNC:24241
    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
    HCCR; HCCR1; HCCR2; HCCR-1; HCCR-2; HCRR-2; SLC55A3; 1110019O13Rik
    Summary
    This gene encodes a mitochondrial outer membrane protein. It has a potential role in tumorigenesis, which may result from negative regulation of the p53 tumor suppressor gene. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.5), fat (RPKM 12.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LETMD1 in Genome Data Viewer
    Location:
    12q13.12
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51048220..51068958)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51011103..51031877)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51442003..51462741)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 11 member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51419127-51419740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51419741-51420352 Neighboring gene RNA, U6 small nuclear 87, pseudogene Neighboring gene RNA, U6 small nuclear 1273, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51441816-51442354 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51442355-51442893 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51463214-51463714 Neighboring gene cysteine and serine rich nuclear protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51477804-51478430 Neighboring gene transcription factor CP2 Neighboring gene ribosomal protein L35a pseudogene 29 Neighboring gene PHB1 pseudogene 19

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp586A011

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular adaptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables molecular adaptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ribosome binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in mitochondrion organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cold-induced thermogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of phagocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in mitochondrial outer membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 

    General protein information

    Preferred Names
    LETM1 domain-containing protein 1
    Names
    cervical cancer 1 proto-oncogene protein p40
    cervical cancer proto-oncogene 2 protein
    epididymis secretory sperm binding protein
    human cervical cancer oncogene
    regulator of TP53

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_029858.3 RefSeqGene

      Range
      5109..17206
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243689.2NP_001230618.1  LETM1 domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001230618.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame donor splice site at an internal exon in the 5' coding region compared to variant 1. This results in a longer isoform (b, also known as 3) containing a 13 aa protein segment not found in isoform 1.
      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS58231.1
      UniProtKB/TrEMBL
      B2RCH7
      Related
      ENSP00000389903.2, ENST00000418425.6
      Conserved Domains (1) summary
      pfam07766
      Location:80351
      LETM1; LETM1-like protein
    2. NM_001300765.2NP_001287694.1  LETM1 domain-containing protein 1 isoform c

      See identical proteins and their annotated locations for NP_001287694.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks three alternate in-frame exons in the central coding region, compared to variant 1. The encoded isoform (c, also known as 7) is shorter than isoform 1.
      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS73469.1
      UniProtKB/TrEMBL
      F8W1Z2
      Related
      ENSP00000447419.1, ENST00000547008.5
      Conserved Domains (1) summary
      pfam07766
      Location:79221
      LETM1; LETM1-like protein
    3. NM_001351312.2NP_001338241.1  LETM1 domain-containing protein 1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), as well as variant 12, encodes isoform d.
      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS44883.1
      UniProtKB/TrEMBL
      B7Z7F8
      Related
      ENSP00000450163.1, ENST00000550929.5
      Conserved Domains (1) summary
      pfam07766
      Location:23289
      LETM1; LETM1-like protein
    4. NM_001351313.2NP_001338242.1  LETM1 domain-containing protein 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), as well as variants 25-27, encodes isoform e.
      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:1188
      LETM1; LETM1-like protein
    5. NM_001351315.2NP_001338244.1  LETM1 domain-containing protein 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B2RCH7
      Conserved Domains (1) summary
      pfam07766
      Location:86352
      LETM1; LETM1-like protein
    6. NM_001351316.2NP_001338245.1  LETM1 domain-containing protein 1 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B2RCH7
      Conserved Domains (1) summary
      pfam07766
      Location:86312
      LETM1; LETM1-like protein
    7. NM_001351317.2NP_001338246.1  LETM1 domain-containing protein 1 isoform h

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B2RCH7
      Conserved Domains (1) summary
      pfam07766
      Location:79305
      LETM1; LETM1-like protein
    8. NM_001351319.2NP_001338248.1  LETM1 domain-containing protein 1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (12), as well as variant 2, encodes isoform d.
      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS44883.1
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:23289
      LETM1; LETM1-like protein
    9. NM_001351320.2NP_001338249.1  LETM1 domain-containing protein 1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      F8VZA2
      Conserved Domains (1) summary
      pfam07766
      Location:23249
      LETM1; LETM1-like protein
    10. NM_001351321.2NP_001338250.1  LETM1 domain-containing protein 1 isoform l

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:79255
      LETM1; LETM1-like protein
    11. NM_001351322.2NP_001338251.1  LETM1 domain-containing protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:1251
      LETM1; LETM1-like protein
    12. NM_001351323.2NP_001338252.1  LETM1 domain-containing protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:1251
      LETM1; LETM1-like protein
    13. NM_001351324.2NP_001338253.1  LETM1 domain-containing protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:1251
      LETM1; LETM1-like protein
    14. NM_001351325.2NP_001338254.1  LETM1 domain-containing protein 1 isoform n

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:116244
      LETM1; LETM1-like protein
    15. NM_001351326.2NP_001338255.1  LETM1 domain-containing protein 1 isoform o

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:37239
      LETM1; LETM1-like protein
    16. NM_001351327.2NP_001338256.1  LETM1 domain-containing protein 1 isoform o

      Status: REVIEWED

      Source sequence(s)
      AC087884
      UniProtKB/TrEMBL
      B7Z7F8
      Conserved Domains (1) summary
      pfam07766
      Location:37239
      LETM1; LETM1-like protein
    17. NM_001351328.2NP_001338257.1  LETM1 domain-containing protein 1 isoform p

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:86228
      LETM1; LETM1-like protein
    18. NM_001351330.2NP_001338259.1  LETM1 domain-containing protein 1 isoform t

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS86301.1
      UniProtKB/TrEMBL
      F8VP71
      Related
      ENSP00000450333.1, ENST00000552739.5
      Conserved Domains (1) summary
      pfam07766
      Location:42228
      LETM1; LETM1-like protein
    19. NM_001351332.2NP_001338261.1  LETM1 domain-containing protein 1 isoform u

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:93228
      LETM1; LETM1-like protein
    20. NM_001351333.2NP_001338262.1  LETM1 domain-containing protein 1 isoform q

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:79181
      LETM1; LETM1-like protein
    21. NM_001351334.2NP_001338263.1  LETM1 domain-containing protein 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (25), as well as variants 4, 26, and 27, encodes isoform e (also called isoform r).
      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:1188
      LETM1; LETM1-like protein
    22. NM_001351335.2NP_001338264.1  LETM1 domain-containing protein 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (26), as well as variants 4, 25, and 27, encodes isoform e (also called isoform r).
      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:1188
      LETM1; LETM1-like protein
    23. NM_001351336.2NP_001338265.1  LETM1 domain-containing protein 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (27), as well as variants 4, 25, and 26, encodes isoform e (also called isoform r).
      Source sequence(s)
      AC087884
      Conserved Domains (1) summary
      pfam07766
      Location:1188
      LETM1; LETM1-like protein
    24. NM_001351337.2NP_001338266.1  LETM1 domain-containing protein 1 isoform s

      Status: REVIEWED

      Source sequence(s)
      AC087884, KF455649
      Conserved Domains (1) summary
      pfam07766
      Location:79181
      LETM1; LETM1-like protein
    25. NM_015416.5NP_056231.3  LETM1 domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_056231.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant protein-coding transcript, and encodes isoform a (also known as HCCR-1 or 1).
      Source sequence(s)
      AC087884
      Consensus CDS
      CCDS8806.1
      UniProtKB/Swiss-Prot
      A6NER7, B3KXK7, Q6P1Q0, Q6X2E4, Q6X2E5, Q7L2G9, Q7L690, Q8WXW6, Q96PK7, Q9BY59, Q9Y3X3
      UniProtKB/TrEMBL
      A0A384P5D7, B2RCH7
      Related
      ENSP00000262055.4, ENST00000262055.9
      Conserved Domains (1) summary
      pfam07766
      Location:79345
      LETM1; LETM1-like protein

    RNA

    1. NR_045019.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two consecutive exons compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with the translation of the longest ORF; translation of the upstream ORF renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC087884
      Related
      ENST00000547318.5
    2. NR_045020.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884, KF455649
    3. NR_147098.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884, BU688852
    4. NR_147099.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    5. NR_147100.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    6. NR_147101.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    7. NR_147102.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    8. NR_147103.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    9. NR_147104.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    10. NR_147105.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    11. NR_147106.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    12. NR_147107.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    13. NR_147108.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    14. NR_147109.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    15. NR_147110.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    16. NR_147111.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    17. NR_147112.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Related
      ENST00000550100.5
    18. NR_147113.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Related
      ENST00000547555.5
    19. NR_147114.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    20. NR_147115.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
      Related
      ENST00000380135.7
    21. NR_147116.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    22. NR_147117.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    23. NR_147118.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    24. NR_147119.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884
    25. NR_147120.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087884

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      51048220..51068958
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428688.1XP_047284644.1  LETM1 domain-containing protein 1 isoform X2

    2. XM_047428687.1XP_047284643.1  LETM1 domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      51011103..51031877
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371706.1XP_054227681.1  LETM1 domain-containing protein 1 isoform X2

    2. XM_054371705.1XP_054227680.1  LETM1 domain-containing protein 1 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001024668.1: Suppressed sequence

      Description
      NM_001024668.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    2. NM_001024669.1: Suppressed sequence

      Description
      NM_001024669.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    3. NM_001024670.1: Suppressed sequence

      Description
      NM_001024670.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    4. NM_001024671.1: Suppressed sequence

      Description
      NM_001024671.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.