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    TMCO3 transmembrane and coiled-coil domains 3 [ Homo sapiens (human) ]

    Gene ID: 55002, updated on 7-Apr-2024

    Summary

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    Official Symbol
    TMCO3provided by HGNC
    Official Full Name
    transmembrane and coiled-coil domains 3provided by HGNC
    Primary source
    HGNC:HGNC:20329
    See related
    Ensembl:ENSG00000150403 MIM:617134; AllianceGenome:HGNC:20329
    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
    C13orf11
    Summary
    This gene encodes a member of the monovalent cation:proton antiporter 2 (CPA2) family of transporter proteins. Members of this family typically couple the export of monovalent cations, such as potassium or sodium, to the import of protons across cellular membranes. Mutations in this gene have been identified in patients with a rare inherited vision defect, cornea guttata with anterior polar cataract. [provided by RefSeq, Mar 2017]
    Expression
    Ubiquitous expression in stomach (RPKM 5.5), endometrium (RPKM 4.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMCO3 in Genome Data Viewer
    Location:
    13q34
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (113491021..113550229)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112749864..112809126)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (114145336..114204544)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114059695-114060489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114061607-114062292 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:114064726-114065925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114071164-114072164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114072165-114073165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114075358-114076070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114076783-114077494 Neighboring gene ADP-ribosylhydrolase like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114080191-114080738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114085068-114085648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114100205-114101146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114105835-114106336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114110333-114111263 Neighboring gene defective in cullin neddylation 1 domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5548 Neighboring gene RNA, U1 small nuclear 16, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr13:114192765-114192953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:114195260-114196459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114200259-114201002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114206049-114206550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114236917-114237890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114237891-114238862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114240840-114241440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114251630-114252130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114267642-114268206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114268207-114268770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114269335-114269898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114269899-114270462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114271027-114271590 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:114271591-114272153 Neighboring gene transcription factor Dp-1 Neighboring gene uncharacterized LOC124903219 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:114279174-114280373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114305936-114306560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114306561-114307185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114311832-114312332 Neighboring gene ATPase H+/K+ transporting subunit beta Neighboring gene G protein-coupled receptor kinase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Mutations in the TMCO3 Gene are Associated with Cornea Guttata and Anterior Polar Cataract. Chen P, et al. Sci Rep, 2016 Aug 3. PMID 27484837, Free PMC Article
    2. Dystonia, facial dysmorphism, intellectual disability and breast cancer associated with a chromosome 13q34 duplication and overexpression of TFDP1: case report. Moscovich M, et al. BMC Med Genet, 2013 Jul 13. PMID 23849371, Free PMC Article
    3. A Novel GLP1 Receptor Interacting Protein ATP6ap2 Regulates Insulin Secretion in Pancreatic Beta Cells. Dai FF, et al. J Biol Chem, 2015 Oct 9. PMID 26272612, Free PMC Article
    4. Regulation of epidermal growth factor receptor trafficking by lysine deacetylase HDAC6. Deribe YL, et al. Sci Signal, 2009 Dec 22. PMID 20029029
    5. The DNA sequence and analysis of human chromosome 13. Dunham A, et al. Nature, 2004 Apr 1. PMID 15057823, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TMCO3, a Putative K[+] :Proton Antiporter at the Golgi Apparatus, Is Important for Longitudinal Growth in Mice and Humans.
      Title: TMCO3, a Putative K(+) :Proton Antiporter at the Golgi Apparatus, Is Important for Longitudinal Growth in Mice and Humans.
    2. This study reveals, for the first time, that mutations in TMCO3 are associated with cornea guttata and anterior polar cataract, warranting further investigation into the pathogenesis of this disorder.
      Title: Mutations in the TMCO3 Gene are Associated with Cornea Guttata and Anterior Polar Cataract.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20623

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables potassium:proton antiporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in potassium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane and coiled-coil domain-containing protein 3
    Names
    putative LAG1-interacting protein

    NCBI Reference Sequences (RefSeq)

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    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_053059.1 RefSeqGene

      Range
      5029..64237
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001349741.2 → NP_001336670.1  transmembrane and coiled-coil domain-containing protein 3 isoform 2 precursor

      Status: REVIEWED

      Source sequence(s)
      AK000630, AK074415, AL442125, BC068515
      Consensus CDS
      CCDS86365.1
      Related
      ENSP00000484053.1, ENST00000474393.5
      Conserved Domains (2) summary
      pfam00999
      Location:274 → 511
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:61 → 253
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_001349742.2 → NP_001336671.1  transmembrane and coiled-coil domain-containing protein 3 isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125
      Conserved Domains (2) summary
      pfam00999
      Location:210 → 581
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:61 → 201
      SMC_N; RecF/RecN/SMC N terminal domain

    3. NM_001349743.2 → NP_001336672.1  transmembrane and coiled-coil domain-containing protein 3 isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125
      Conserved Domains (2) summary
      cl01133
      Location:210 → 283
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:26 → 213
      SMC_N; RecF/RecN/SMC N terminal domain

    4. NM_001349744.2 → NP_001336673.1  transmembrane and coiled-coil domain-containing protein 3 isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125
      Conserved Domains (2) summary
      pfam00999
      Location:274 → 560
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:61 → 253
      SMC_N; RecF/RecN/SMC N terminal domain

    5. NM_001349745.2 → NP_001336674.1  transmembrane and coiled-coil domain-containing protein 3 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125
      Conserved Domains (2) summary
      pfam00999
      Location:210 → 496
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:26 → 201
      SMC_N; RecF/RecN/SMC N terminal domain

    6. NM_001349746.2 → NP_001336675.1  transmembrane and coiled-coil domain-containing protein 3 isoform 7 precursor

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125
      Conserved Domains (2) summary
      cl01133
      Location:274 → 347
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      cl25732
      Location:26 → 253
      SMC_N; RecF/RecN/SMC N terminal domain

    7. NM_017905.6 → NP_060375.4  transmembrane and coiled-coil domain-containing protein 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_060375.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK074415, BC068515
      Consensus CDS
      CCDS9537.1
      UniProtKB/Swiss-Prot
      Q5JSB1, Q6NUN1, Q6UWJ1, Q8NG29, Q8TCI6, Q96EA6, Q9NWT2
      UniProtKB/TrEMBL
      A0A024RE09
      Related
      ENSP00000389399.2, ENST00000434316.7
      Conserved Domains (2) summary
      pfam00999
      Location:274 → 645
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      pfam01519
      Location:88 → 195
      DUF16; Protein of unknown function DUF16

    RNA

    1. NR_146221.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125

    2. NR_146222.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK074415, AL442125

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      113491021..113550229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430398.1 → XP_047286354.1  transmembrane and coiled-coil domain-containing protein 3 isoform X1

    2. XM_047430399.1 → XP_047286355.1  transmembrane and coiled-coil domain-containing protein 3 isoform X2

    3. XM_047430404.1 → XP_047286360.1  transmembrane and coiled-coil domain-containing protein 3 isoform X7

    4. XM_047430407.1 → XP_047286363.1  transmembrane and coiled-coil domain-containing protein 3 isoform X10

    5. XM_047430402.1 → XP_047286358.1  transmembrane and coiled-coil domain-containing protein 3 isoform X5

    6. XM_047430403.1 → XP_047286359.1  transmembrane and coiled-coil domain-containing protein 3 isoform X6

    7. XM_047430408.1 → XP_047286364.1  transmembrane and coiled-coil domain-containing protein 3 isoform X11

    8. XM_006719969.2 → XP_006720032.1  transmembrane and coiled-coil domain-containing protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006720032.1

      UniProtKB/Swiss-Prot
      Q5JSB1, Q6NUN1, Q6UWJ1, Q8NG29, Q8TCI6, Q96EA6, Q9NWT2
      UniProtKB/TrEMBL
      A0A024RE09
      Conserved Domains (2) summary
      pfam00999
      Location:274 → 645
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      pfam01519
      Location:88 → 195
      DUF16; Protein of unknown function DUF16

    9. XM_047430401.1 → XP_047286357.1  transmembrane and coiled-coil domain-containing protein 3 isoform X4

    10. XM_047430410.1 → XP_047286366.1  transmembrane and coiled-coil domain-containing protein 3 isoform X12

    11. XM_047430409.1 → XP_047286365.1  transmembrane and coiled-coil domain-containing protein 3 isoform X12

    12. XM_047430406.1 → XP_047286362.1  transmembrane and coiled-coil domain-containing protein 3 isoform X9

    13. XM_047430414.1 → XP_047286370.1  transmembrane and coiled-coil domain-containing protein 3 isoform X16

    14. XM_047430405.1 → XP_047286361.1  transmembrane and coiled-coil domain-containing protein 3 isoform X8

    15. XM_047430411.1 → XP_047286367.1  transmembrane and coiled-coil domain-containing protein 3 isoform X13

    16. XM_047430413.1 → XP_047286369.1  transmembrane and coiled-coil domain-containing protein 3 isoform X15

      Related
      ENSP00000364540.1, ENST00000375391.5

    17. XM_047430412.1 → XP_047286368.1  transmembrane and coiled-coil domain-containing protein 3 isoform X14

    18. XM_047430415.1 → XP_047286371.1  transmembrane and coiled-coil domain-containing protein 3 isoform X17

    19. XM_047430400.1 → XP_047286356.1  transmembrane and coiled-coil domain-containing protein 3 isoform X4

    20. XM_011537498.3 → XP_011535800.1  transmembrane and coiled-coil domain-containing protein 3 isoform X3

      See identical proteins and their annotated locations for XP_011535800.1

      UniProtKB/Swiss-Prot
      Q5JSB1, Q6NUN1, Q6UWJ1, Q8NG29, Q8TCI6, Q96EA6, Q9NWT2
      UniProtKB/TrEMBL
      A0A024RE09
      Conserved Domains (2) summary
      pfam00999
      Location:274 → 645
      Na_H_Exchanger; Sodium/hydrogen exchanger family
      pfam01519
      Location:88 → 195
      DUF16; Protein of unknown function DUF16

    RNA

    1. XR_007063685.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      112749864..112809126
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374616.1 → XP_054230591.1  transmembrane and coiled-coil domain-containing protein 3 isoform X1

    2. XM_054374621.1 → XP_054230596.1  transmembrane and coiled-coil domain-containing protein 3 isoform X4

    3. XM_054374618.1 → XP_054230593.1  transmembrane and coiled-coil domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      Q5JSB1, Q6NUN1, Q6UWJ1, Q8NG29, Q8TCI6, Q96EA6, Q9NWT2
      UniProtKB/TrEMBL
      A0A024RE09

    4. XM_054374627.1 → XP_054230602.1  transmembrane and coiled-coil domain-containing protein 3 isoform X11

    5. XM_054374625.1 → XP_054230600.1  transmembrane and coiled-coil domain-containing protein 3 isoform X8

    6. XM_054374623.1 → XP_054230598.1  transmembrane and coiled-coil domain-containing protein 3 isoform X6

    7. XM_054374622.1 → XP_054230597.1  transmembrane and coiled-coil domain-containing protein 3 isoform X5

    8. XM_054374624.1 → XP_054230599.1  transmembrane and coiled-coil domain-containing protein 3 isoform X7

    9. XM_054374617.1 → XP_054230592.1  transmembrane and coiled-coil domain-containing protein 3 isoform X2

    10. XM_054374629.1 → XP_054230604.1  transmembrane and coiled-coil domain-containing protein 3 isoform X12

    11. XM_054374626.1 → XP_054230601.1  transmembrane and coiled-coil domain-containing protein 3 isoform X9

    12. XM_054374628.1 → XP_054230603.1  transmembrane and coiled-coil domain-containing protein 3 isoform X12

    13. XM_054374630.1 → XP_054230605.1  transmembrane and coiled-coil domain-containing protein 3 isoform X13

    14. XM_054374631.1 → XP_054230606.1  transmembrane and coiled-coil domain-containing protein 3 isoform X14

    15. XM_054374632.1 → XP_054230607.1  transmembrane and coiled-coil domain-containing protein 3 isoform X15

    16. XM_054374633.1 → XP_054230608.1  transmembrane and coiled-coil domain-containing protein 3 isoform X17

    17. XM_054374620.1 → XP_054230595.1  transmembrane and coiled-coil domain-containing protein 3 isoform X4

    18. XM_054374619.1 → XP_054230594.1  transmembrane and coiled-coil domain-containing protein 3 isoform X3

      UniProtKB/Swiss-Prot
      Q5JSB1, Q6NUN1, Q6UWJ1, Q8NG29, Q8TCI6, Q96EA6, Q9NWT2
      UniProtKB/TrEMBL
      A0A024RE09
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWJ1.1 GenPept UniProtKB/Swiss-Prot:Q6UWJ1

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