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    GRAMD1A GRAM domain containing 1A [ Homo sapiens (human) ]

    Gene ID: 57655, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GRAMD1Aprovided by HGNC
    Official Full Name
    GRAM domain containing 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:29305
    See related
    Ensembl:ENSG00000089351 MIM:620178; AllianceGenome:HGNC:29305
    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
    KIAA1533
    Summary
    Predicted to enable cholesterol binding activity and cholesterol transfer activity. Predicted to be involved in cellular response to cholesterol and intracellular sterol transport. Located in several cellular components, including cytosol; endoplasmic reticulum membrane; and organelle membrane contact site. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lung (RPKM 13.7), spleen (RPKM 13.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GRAMD1A in Genome Data Viewer
    Location:
    19q13.11
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (34994727..35026469)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (37539338..37571085)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (35485631..35517373)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10511 Neighboring gene zinc finger protein 792 Neighboring gene uncharacterized LOC124904700 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:35488612-35489287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35495135-35495680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35495681-35496225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10514 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:35521843-35521951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:35531257-35532096 Neighboring gene sodium voltage-gated channel beta subunit 1 Neighboring gene hepsin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35556563-35557324 Neighboring gene HPN antisense RNA 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 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. GRAM domain-containing protein 1A (GRAMD1A) promotes the expansion of hepatocellular carcinoma stem cell and hepatocellular carcinoma growth through STAT5. Fu B, et al. Sci Rep, 2016 Sep 2. PMID 27585821, Free PMC Article
    2. GRAMD1A Is a Biomarker of Kidney Renal Clear Cell Carcinoma and Is Associated with Immune Infiltration in the Tumour Microenvironment. Liu Y, et al. Dis Markers, 2022. PMID 35860689, Free PMC Article
    3. GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells. Besprozvannaya M, et al. Elife, 2018 Feb 22. PMID 29469807, Free PMC Article
    4. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
    5. Spatial proteomics reveal that the protein phosphatase PTP1B interacts with and may modify tyrosine phosphorylation of the rhomboid protease RHBDL4. Ikeda KN, et al. J Biol Chem, 2019 Jul 26. PMID 31177093, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GRAMD1A Is a Biomarker of Kidney Renal Clear Cell Carcinoma and Is Associated with Immune Infiltration in the Tumour Microenvironment.
      Title: GRAMD1A Is a Biomarker of Kidney Renal Clear Cell Carcinoma and Is Associated with Immune Infiltration in the Tumour Microenvironment.
    2. GRAMD2a, but not GRAMD1a, co-localizes with the E-Syt2/3 tethers at endoplasmic reticulum-plasma membrane contact sites in a phosphatidylinositol phosphate lipid-dependent manner. Data from an analysis of cells lacking GRAMD2a suggest that it is an organizer of the membrane contact sites with pleiotropic functions including calcium homeostasis.
      Title: GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells.
    3. STAT5 was the target of GRAMD1A; GRAMD1A regulated the target genes of STAT5 and the transcriptional activity of STAT5. Inhibition of STAT5 in indicated HCC cells overexpressing GRAMD1A suppressed the effects of GRAMD1A on the self-renewal of HCC stem cell, resistance to chemotherapy and tumor growth, suggesting GRAMD1A promoted the self-renewal of HCC stem cells and the development of HCC by increasing STAT5 level.
      Title: GRAM domain-containing protein 1A (GRAMD1A) promotes the expansion of hepatocellular carcinoma stem cell and hepatocellular carcinoma growth through STAT5.
    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

    • FLJ22411, FLJ90346

    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 autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    located_in autophagosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    located_in organelle membrane contact site 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 

    General protein information

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

    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_001136199.3 → NP_001129671.1  protein Aster-A isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is 11 amino acids shorter than isoform 1.
      Source sequence(s)
      AK074827, AK074914, BC041618, CD367242, DA390646
      Consensus CDS
      CCDS46046.1
      UniProtKB/TrEMBL
      B3KUH3
      Related
      ENSP00000439267.1, ENST00000411896.6
      Conserved Domains (2) summary
      cd13220
      Location:95 → 188
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:363 → 509
      DUF4782; Domain of unknown function (DUF4782)

    2. NM_001320034.2 → NP_001306963.1  protein Aster-A isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (3) has the same N- and C-termini, but is four amino acids shorter than isoform 1.
      Source sequence(s)
      AB040966, BC014077, CD367242, DA390646
      Consensus CDS
      CCDS92585.1
      UniProtKB/TrEMBL
      B3KUH3
      Related
      ENSP00000505404.1, ENST00000680623.1
      Conserved Domains (2) summary
      cd13220
      Location:102 → 195
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:370 → 516
      DUF4782; Domain of unknown function (DUF4782)

    3. NM_001320035.2 → NP_001306964.1  protein Aster-A isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon compared to variant 1. This variant represents translation initiation at an alternate start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the alternate start codon to encode an isoform (4) that has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK074864, BC014077, CD367242, DA390646
      UniProtKB/TrEMBL
      B3KQF7
      Conserved Domains (1) summary
      pfam16016
      Location:141 → 284
      DUF4782; Domain of unknown function (DUF4782)

    4. NM_001320036.2 → NP_001306965.1  protein Aster-A isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains two alternate exons in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at an alternate start codon, and uses an alternate in-frame splice site in the central coding region compared to variant 1. The encoded isoform (5) has a longer and distinct N-terminus and lacks an internal amino acid, compared to isoform 1.
      Source sequence(s)
      AB040966, AC020907, AK097215, BC014077, CD367242
      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:189 → 282
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:456 → 602
      DUF4782; Domain of unknown function (DUF4782)

    5. NM_020895.5 → NP_065946.2  protein Aster-A isoform 1

      See identical proteins and their annotated locations for NP_065946.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AB040966, BC014077, CD367242, DA390646
      Consensus CDS
      CCDS42546.1
      UniProtKB/Swiss-Prot
      A6NKY7, Q8NC77, Q96CP6, Q9P1Z5
      UniProtKB/TrEMBL
      B3KUH3
      Related
      ENSP00000441032.1, ENST00000317991.10
      Conserved Domains (2) summary
      cd13220
      Location:102 → 195
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:370 → 516
      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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      34994727..35026469
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527153.2 → XP_011525455.1  protein Aster-A isoform X4

      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:189 → 282
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:462 → 605
      DUF4782; Domain of unknown function (DUF4782)

    2. XM_017027035.2 → XP_016882524.1  protein Aster-A isoform X3

      UniProtKB/TrEMBL
      B3KUH3, M0QZ12
      Related
      ENSP00000470220.1, ENST00000599564.5
      Conserved Domains (2) summary
      cd13220
      Location:189 → 282
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:462 → 605
      DUF4782; Domain of unknown function (DUF4782)

    3. XM_047439133.1 → XP_047295089.1  protein Aster-A isoform X5

    4. XM_017027034.3 → XP_016882523.1  protein Aster-A isoform X2

      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:102 → 195
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:375 → 518
      DUF4782; Domain of unknown function (DUF4782)

    5. XM_011527149.3 → XP_011525451.1  protein Aster-A isoform X1

      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:102 → 195
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:374 → 517
      DUF4782; Domain of unknown function (DUF4782)

    6. XM_024451622.2 → XP_024307390.1  protein Aster-A isoform X6

      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:63 → 156
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:336 → 479
      DUF4782; Domain of unknown function (DUF4782)

    7. XM_011527155.2 → XP_011525457.1  protein Aster-A isoform X5

      UniProtKB/TrEMBL
      B3KUH3
      Conserved Domains (2) summary
      cd13220
      Location:107 → 200
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16016
      Location:380 → 523
      DUF4782; Domain of unknown function (DUF4782)

    8. XM_047439134.1 → XP_047295090.1  protein Aster-A isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      37539338..37571085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321549.1 → XP_054177524.1  protein Aster-A isoform X4

    2. XM_054321550.1 → XP_054177525.1  protein Aster-A isoform X9

    3. XM_054321548.1 → XP_054177523.1  protein Aster-A isoform X3

    4. XM_054321547.1 → XP_054177522.1  protein Aster-A isoform X8

    5. XM_054321556.1 → XP_054177531.1  protein Aster-A isoform X10

    6. XM_054321552.1 → XP_054177527.1  protein Aster-A isoform X5

    7. XM_054321554.1 → XP_054177529.1  protein Aster-A isoform X6

    8. XM_054321551.1 → XP_054177526.1  protein Aster-A isoform X5

    9. XM_054321553.1 → XP_054177528.1  protein Aster-A isoform X6

    10. XM_054321555.1 → XP_054177530.1  protein Aster-A isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96CP6.2 GenPept UniProtKB/Swiss-Prot:Q96CP6

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