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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
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Genomic context

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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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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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