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    GRAMD1C GRAM domain containing 1C [ Homo sapiens (human) ]

    Gene ID: 54762, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GRAMD1Cprovided by HGNC
    Official Full Name
    GRAM domain containing 1Cprovided by HGNC
    Primary source
    HGNC:HGNC:25252
    See related
    Ensembl:ENSG00000178075 MIM:620180; AllianceGenome:HGNC:25252
    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
    Summary
    Predicted to enable cholesterol binding activity and cholesterol transfer activity. Predicted to be involved in cellular response to cholesterol and intracellular sterol transport. Predicted to be located in endoplasmic reticulum; membrane; and organelle membrane contact site. Predicted to be active in endoplasmic reticulum membrane; endoplasmic reticulum-plasma membrane contact site; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in kidney (RPKM 8.8), testis (RPKM 8.7) and 21 other tissues See more
    Orthologs
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    Genomic context

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    See GRAMD1C in Genome Data Viewer
    Location:
    3q13.31
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (113828192..113947174)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (116549379..116668438)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (113557635..113666021)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113463940-113464676 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113464677-113465412 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113465413-113466148 Neighboring gene N-alpha-acetyltransferase 50, NatE catalytic subunit Neighboring gene ATPase H+ transporting V1 subunit A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14611 Neighboring gene ribosomal protein S10 pseudogene 4 Neighboring gene CTDNEP1 pseudogene 1 Neighboring gene VPS26A pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:113666278-113666778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14613 Neighboring gene zinc finger DHHC-type palmitoyltransferase 23 Neighboring gene coiled-coil domain containing 191 Neighboring gene ATP5PB pseudogene 8

    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 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. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
    2. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article
    3. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article
    4. Widespread macromolecular interaction perturbations in human genetic disorders. Sahni N, et al. Cell, 2015 Apr 23. PMID 25910212, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35862, FLJ40464, DKFZp434C0328, DKFZp686K06117

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cholesterol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cholesterol binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables cholesterol transfer activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cholesterol transfer 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 cellular response to cholesterol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intracellular sterol transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in endoplasmic reticulum-plasma membrane contact site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum-plasma membrane contact site ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    protein Aster-C
    Names
    Aster-C
    GRAM domain-containing protein 1C

    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_001172105.2 → NP_001165576.1  protein Aster-C isoform 2

      See identical proteins and their annotated locations for NP_001165576.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses a downstream start codon, compared to variant 1. The resulting isoform (2) has a substantially shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK292964, AL133661, BX648633, DC416411
      Consensus CDS
      CCDS54625.1
      UniProtKB/TrEMBL
      E9PHT3
      Related
      ENSP00000408135.2, ENST00000440446.2
      Conserved Domains (1) summary
      pfam16016
      Location:128 → 271
      DUF4782; Domain of unknown function (DUF4782)

    2. NM_017577.5 → NP_060047.3  protein Aster-C isoform 1

      See identical proteins and their annotated locations for NP_060047.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC079944, AK292846, BC035040, CV575069
      Consensus CDS
      CCDS33826.1
      UniProtKB/Swiss-Prot
      A8K9Y1, A8KA99, Q6AW94, Q6UWN1, Q8IYS0, Q8N6S0, Q9UF46
      Related
      ENSP00000350881.4, ENST00000358160.9
      Conserved Domains (2) summary
      cd13220
      Location:80 → 173
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:329 → 476
      DUF4782; Domain of unknown function (DUF4782)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      113828192..113947174
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512930.2 → XP_011511232.1  protein Aster-C isoform X1

      Conserved Domains (2) summary
      cd13220
      Location:70 → 163
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:323 → 466
      DUF4782; Domain of unknown function (DUF4782)

    2. XM_005247547.3 → XP_005247604.1  protein Aster-C isoform X2

      Conserved Domains (2) summary
      cd13220
      Location:80 → 173
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:333 → 476
      DUF4782; Domain of unknown function (DUF4782)

    3. XM_011512931.2 → XP_011511233.1  protein Aster-C isoform X3

      See identical proteins and their annotated locations for XP_011511233.1

      UniProtKB/TrEMBL
      E9PHT3
      Related
      ENSP00000419132.1, ENST00000472026.5
      Conserved Domains (1) summary
      pfam16016
      Location:128 → 271
      DUF4782; Domain of unknown function (DUF4782)

    4. XM_017006649.2 → XP_016862138.1  protein Aster-C isoform X4

      UniProtKB/TrEMBL
      B3KUR5
      Conserved Domains (1) summary
      pfam16016
      Location:62 → 205
      DUF4782; Domain of unknown function (DUF4782)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      116549379..116668438
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346955.1 → XP_054202930.1  protein Aster-C isoform X1

    2. XM_054346956.1 → XP_054202931.1  protein Aster-C isoform X2

    3. XM_054346957.1 → XP_054202932.1  protein Aster-C isoform X3

    4. XM_054346958.1 → XP_054202933.1  protein Aster-C isoform X4

      UniProtKB/TrEMBL
      B3KUR5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYS0.2 GenPept UniProtKB/Swiss-Prot:Q8IYS0

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