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    TMEM63A transmembrane protein 63A [ Homo sapiens (human) ]

    Gene ID: 9725, updated on 3-May-2024

    Summary

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    Official Symbol
    TMEM63Aprovided by HGNC
    Official Full Name
    transmembrane protein 63Aprovided by HGNC
    Primary source
    HGNC:HGNC:29118
    See related
    Ensembl:ENSG00000196187 MIM:618685; AllianceGenome:HGNC:29118
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HLD19; KIAA0792
    Summary
    Enables mechanosensitive ion channel activity. Predicted to be involved in cation transmembrane transport. Located in centriolar satellite and lysosomal membrane. Implicated in hypomyelinating leukodystrophy. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in salivary gland (RPKM 15.4), prostate (RPKM 13.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM63A in Genome Data Viewer
    Location:
    1q42.12
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (225840556..225882380, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225028653..225070125, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (226033237..226070080, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:225969251-225969750 Neighboring gene signal recognition particle 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1859 Neighboring gene left-right determination factor 3, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226004679-226005506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226005507-226006333 Neighboring gene epoxide hydrolase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226012583-226013259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226015269-226016122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226033607-226034417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2630 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:226037931-226038477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2631 Neighboring gene MPRA-validated peak731 silencer Neighboring gene MPRA-validated peak732 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226067686-226068636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226074845-226075561 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226077715-226078432 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:226078433-226079150 and GRCh37_chr1:226079151-226079866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226083967-226084730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2635 Neighboring gene left-right determination factor 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226087020-226087782 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:226087783-226088545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226094136-226094909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226102994-226103938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226103939-226104881 Neighboring gene microRNA 6741 Neighboring gene pyrroline-5-carboxylate reductase 2

    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. Spinal cord involvement and paroxysmal events in "Infantile Onset Transient Hypomyelination" due to TMEM63A mutation. Tonduti D, et al. J Hum Genet, 2021 Oct. PMID 33785861
    2. The N- and C-terminal carbohydrate recognition domains of Haemonchus contortus galectin bind to distinct receptors of goat PBMC and contribute differently to its immunomodulatory functions in host-parasite interactions. Lu M, et al. Parasit Vectors, 2017 Sep 5. PMID 28870237, Free PMC Article
    3. Heterozygous Variants in the Mechanosensitive Ion Channel TMEM63A Result in Transient Hypomyelination during Infancy. Yan H, et al. Am J Hum Genet, 2019 Nov 7. PMID 31587869, Free PMC Article
    4. The proteome of lysosomes. Schröder BA, et al. Proteomics, 2010 Nov. PMID 20957757
    5. OSCA/TMEM63 are an Evolutionarily Conserved Family of Mechanically Activated Ion Channels. Murthy SE, et al. Elife, 2018 Nov 1. PMID 30382938, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Stretch response of the mechano-gated channel TMEM63A in membrane patches and single cells.
      Title: Stretch response of the mechano-gated channel TMEM63A in membrane patches and single cells.
    2. Spinal cord involvement and paroxysmal events in ""Infantile Onset Transient Hypomyelination"" due to TMEM63A mutation.
      Title: Spinal cord involvement and paroxysmal events in "Infantile Onset Transient Hypomyelination" due to TMEM63A mutation.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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

    Associated conditions

    Description Tests
    Leukodystrophy, hypomyelinating, 19, transient infantile
    MedGen: C5231463 OMIM: 618688 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of transmembrane protein 63A (TMEM63A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0489

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium-activated cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mechanosensitive monoatomic ion channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mechanosensitive monoatomic ion channel activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables osmolarity-sensing monoatomic cation channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in monoatomic cation transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in surfactant secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		  
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in lysosomal membrane HDA PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in tertiary granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    CSC1-like 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.

    mRNA and Protein(s)

    1. NM_014698.3 → NP_055513.2  CSC1-like protein 1

      See identical proteins and their annotated locations for NP_055513.2

      Status: VALIDATED

      Source sequence(s)
      AB018335, AL117348, AL591895, BF512395, DA127076
      Consensus CDS
      CCDS31042.1
      UniProtKB/Swiss-Prot
      O94886, Q53GI7, Q5TE96, Q8N2U2
      UniProtKB/TrEMBL
      B3KMR6
      Related
      ENSP00000355800.3, ENST00000366835.8
      Conserved Domains (3) summary
      pfam02714
      Location:439 → 692
      RSN1_7TM; Calcium-dependent channel, 7TM region, putative phosphate
      pfam13967
      Location:52 → 207
      RSN1_TM; Late exocytosis, associated with Golgi transport
      pfam14703
      Location:228 → 410
      PHM7_cyt; Cytosolic domain of 10TM putative phosphate transporter

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      225840556..225882380 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544330.4 → XP_011542632.1  CSC1-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011542632.1

      UniProtKB/Swiss-Prot
      O94886, Q53GI7, Q5TE96, Q8N2U2
      UniProtKB/TrEMBL
      B3KMR6
      Conserved Domains (3) summary
      pfam02714
      Location:439 → 692
      RSN1_7TM; Calcium-dependent channel, 7TM region, putative phosphate
      pfam13967
      Location:52 → 207
      RSN1_TM; Late exocytosis, associated with Golgi transport
      pfam14703
      Location:228 → 410
      PHM7_cyt; Cytosolic domain of 10TM putative phosphate transporter

    2. XM_047435144.1 → XP_047291100.1  CSC1-like protein 1 isoform X2

    3. XM_047435146.1 → XP_047291102.1  CSC1-like protein 1 isoform X4

    4. XM_047435145.1 → XP_047291101.1  CSC1-like protein 1 isoform X3

    5. XM_047435148.1 → XP_047291104.1  CSC1-like protein 1 isoform X5

    RNA

    1. XR_007065257.1 RNA Sequence

    2. XR_949163.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      225028653..225070125 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339766.1 → XP_054195741.1  CSC1-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O94886, Q53GI7, Q5TE96, Q8N2U2

    2. XM_054339767.1 → XP_054195742.1  CSC1-like protein 1 isoform X2

    3. XM_054339769.1 → XP_054195744.1  CSC1-like protein 1 isoform X4

    4. XM_054339768.1 → XP_054195743.1  CSC1-like protein 1 isoform X3

    RNA

    1. XR_008486220.1 RNA Sequence

    2. XR_008486218.1 RNA Sequence

    3. XR_008486219.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94886.3 GenPept UniProtKB/Swiss-Prot:O94886

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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