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

Gene ID: 9725, updated on 3-Apr-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
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Genomic context

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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
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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
  
Component Evidence Code Pubs
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
  
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

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