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

Gene ID: 57655, updated on 28-Oct-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, Oct 2024]
Expression
Ubiquitous expression in lung (RPKM 13.7), spleen (RPKM 13.3) and 25 other tissues See more
Orthologs
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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

Gene LinkOut

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