Aliases for GRAMD1B Gene

Aliases for GRAMD1B Gene

  • GRAM Domain Containing 1B 2 3 5
  • Long Intergenic Non-Protein Coding RNA 1059 2 3
  • GRAM Domain-Containing Protein 1B 3 4
  • Protein Aster-B 3 4
  • LINC01059 3
  • KIAA1201 4

External Ids for GRAMD1B Gene

Previous HGNC Symbols for GRAMD1B Gene

  • LINC01059

Previous GeneCards Identifiers for GRAMD1B Gene

  • GC11P122903
  • GC11U900713
  • GC11P123396
  • GC11P119338

Summaries for GRAMD1B Gene

GeneCards Summary for GRAMD1B Gene

GRAMD1B (GRAM Domain Containing 1B) is a Protein Coding gene. Among its related pathways are Ectoderm Differentiation. An important paralog of this gene is GRAMD1A.

UniProtKB/Swiss-Prot Summary for GRAMD1B Gene

  • Cholesterol transporter that mediates non-vesicular transport of cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER) (By similarity). Contains unique domains for binding cholesterol and the PM, thereby serving as a molecular bridge for the transfer of cholesterol from the PM to the ER (By similarity). Plays a crucial role in cholesterol homeostasis in the adrenal gland and has the unique ability to localize to the PM based on the level of membrane cholesterol (By similarity). In lipid-poor conditions localizes to the ER membrane and in response to excess cholesterol in the PM is recruited to the endoplasmic reticulum-plasma membrane contact sites (EPCS) which is mediated by the GRAM domain (By similarity). At the EPCS, the sterol-binding VASt/ASTER domain binds to the cholesterol in the PM and facilitates its transfer from the PM to ER (By similarity).

Additional gene information for GRAMD1B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GRAMD1B Gene

Genomics for GRAMD1B Gene

GeneHancer (GH) Regulatory Elements for GRAMD1B Gene

Promoters and enhancers for GRAMD1B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J123559 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.1 +202.3 202320 3.4 ZBTB40 CTCF MYC CREM POLR2A NRF1 EED USF1 RCOR1 GATA3 GRAMD1B SF3A3P2 lnc-OR8D4-1
GH11J123357 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas 750.6 +0.1 119 1.7 CTCF ZNF701 ETV6 NKRF POLR2A MLLT1 PRDM1 CREM IKZF1 ZBTB8A GRAMD1B lnc-JHY-7 CLMP ZNF202
GH11J123525 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.1 +167.2 167219 1.5 GATA3 GRAMD1B SF3A3P2 lnc-OR8D4-1
GH11J123509 Enhancer 1.5 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 23.4 +152.4 152373 3.2 CTCF ZBTB6 HLF RAD21 SP1 ZSCAN21 PRDM1 PKNOX1 ZNF512 TRIM22 GRAMD1B ATP5PBP5 SCN3B lnc-OR8D4-1 SF3A3P2
GH11J123449 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 18.3 +95.9 95923 9.3 SIN3A LCORL POLR2A ZNF133 JUND MYC ETV6 ELF1 MAX NFIB lnc-OR8D4-1 GRAMD1B ZNF202 MIR4493
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GRAMD1B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GRAMD1B gene promoter:
  • AhR
  • Arnt
  • Bach1
  • FOXL1
  • GATA-2
  • Lmo2
  • MIF-1
  • Nkx2-5
  • Pax-5
  • POU6F1 (c2)

Genomic Locations for GRAMD1B Gene

Genomic Locations for GRAMD1B Gene
chr11:123,358,428-123,627,774
(GRCh38/hg38)
Size:
269,347 bases
Orientation:
Plus strand
chr11:123,396,344-123,498,482
(GRCh37/hg19)
Size:
102,139 bases
Orientation:
Plus strand

Genomic View for GRAMD1B Gene

Genes around GRAMD1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GRAMD1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GRAMD1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GRAMD1B Gene

Proteins for GRAMD1B Gene

  • Protein details for GRAMD1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3KR37-ASTRB_HUMAN
    Recommended name:
    Protein Aster-B
    Protein Accession:
    Q3KR37
    Secondary Accessions:
    • B3KXJ5
    • E7EPH8
    • Q6UW85
    • Q9ULL9

    Protein attributes for GRAMD1B Gene

    Size:
    738 amino acids
    Molecular mass:
    85400 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA86515.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for GRAMD1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GRAMD1B Gene

Post-translational modifications for GRAMD1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GRAMD1B Gene

Domains & Families for GRAMD1B Gene

Gene Families for GRAMD1B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for GRAMD1B Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GRAMD1B Gene

GenScript: Design optimal peptide antigens:
  • GRAM domain-containing protein 1B (GRM1B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q3KR37

UniProtKB/Swiss-Prot:

ASTRB_HUMAN :
  • GRAM domain binds phosphatidylserine in the PM and mediates protein recruitment to endoplasmic reticulum-plasma membrane contact sites (EPCS) in response to excess cholesterol in the PM.
Domain:
  • GRAM domain binds phosphatidylserine in the PM and mediates protein recruitment to endoplasmic reticulum-plasma membrane contact sites (EPCS) in response to excess cholesterol in the PM.
  • VASt (VAD1 Analog of StAR-related lipid transfer) domain, also known as ASTER (Greek for star) domain is a sterol-binding domain.
genes like me logo Genes that share domains with GRAMD1B: view

Function for GRAMD1B Gene

Molecular function for GRAMD1B Gene

UniProtKB/Swiss-Prot Function:
Cholesterol transporter that mediates non-vesicular transport of cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER) (By similarity). Contains unique domains for binding cholesterol and the PM, thereby serving as a molecular bridge for the transfer of cholesterol from the PM to the ER (By similarity). Plays a crucial role in cholesterol homeostasis in the adrenal gland and has the unique ability to localize to the PM based on the level of membrane cholesterol (By similarity). In lipid-poor conditions localizes to the ER membrane and in response to excess cholesterol in the PM is recruited to the endoplasmic reticulum-plasma membrane contact sites (EPCS) which is mediated by the GRAM domain (By similarity). At the EPCS, the sterol-binding VASt/ASTER domain binds to the cholesterol in the PM and facilitates its transfer from the PM to ER (By similarity).

Phenotypes From GWAS Catalog for GRAMD1B Gene

Gene Ontology (GO) - Molecular Function for GRAMD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001786 phosphatidylserine binding ISS --
GO:0008289 lipid binding IEA --
GO:0015485 cholesterol binding ISS --
GO:0070300 phosphatidic acid binding ISS --
GO:0120020 intermembrane cholesterol transfer activity ISS --
genes like me logo Genes that share ontologies with GRAMD1B: view
genes like me logo Genes that share phenotypes with GRAMD1B: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GRAMD1B Gene

Localization for GRAMD1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for GRAMD1B Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Cell membrane; Single-pass membrane protein. Note=In lipid-poor conditions localizes to the ER membrane and in response to excess cholesterol in the PM is recruited to the endoplasmic reticulum-plasma membrane contact sites (EPCS). {ECO:0000269 PubMed:30220461}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GRAMD1B gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
nucleus 3
cytoskeleton 2
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GRAMD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IDA,IEA 30220461
GO:0005886 plasma membrane IEA,IDA 30220461
GO:0016020 membrane HDA,IEA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with GRAMD1B: view

Pathways & Interactions for GRAMD1B Gene

PathCards logo

SuperPathways for GRAMD1B Gene

SuperPathway Contained pathways
1 Ectoderm Differentiation
genes like me logo Genes that share pathways with GRAMD1B: view

Pathways by source for GRAMD1B Gene

1 BioSystems pathway for GRAMD1B Gene

Gene Ontology (GO) - Biological Process for GRAMD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IEA --
GO:0015918 sterol transport IEA --
GO:0030301 cholesterol transport IEA --
GO:0042632 cholesterol homeostasis ISS --
GO:0071397 cellular response to cholesterol ISS --
genes like me logo Genes that share ontologies with GRAMD1B: view

No data available for SIGNOR curated interactions for GRAMD1B Gene

Drugs & Compounds for GRAMD1B Gene

(1) Drugs for GRAMD1B Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
lithium Experimental Pharma 0
genes like me logo Genes that share compounds with GRAMD1B: view

Transcripts for GRAMD1B Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GRAMD1B Gene

No ASD Table

Relevant External Links for GRAMD1B Gene

GeneLoc Exon Structure for
GRAMD1B
ECgene alternative splicing isoforms for
GRAMD1B

Expression for GRAMD1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GRAMD1B Gene

mRNA differential expression in normal tissues according to GTEx for GRAMD1B Gene

This gene is overexpressed in Brain - Cerebellum (x8.7), Brain - Cerebellar Hemisphere (x8.3), and Adrenal Gland (x6.3).

Protein differential expression in normal tissues from HIPED for GRAMD1B Gene

This gene is overexpressed in Adrenal (45.1) and Testis (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GRAMD1B Gene



Protein tissue co-expression partners for GRAMD1B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GRAMD1B Gene:

GRAMD1B

SOURCE GeneReport for Unigene cluster for GRAMD1B Gene:

Hs.144725

Evidence on tissue expression from TISSUES for GRAMD1B Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with GRAMD1B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GRAMD1B Gene

Orthologs for GRAMD1B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GRAMD1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GRAMD1B 33 32
  • 97.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GRAMD1B 33 32
  • 93.33 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GRAMD1B 33 32
  • 91.97 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gramd1b 17 33 32
  • 90.77 (n)
rat
(Rattus norvegicus)
Mammalia Gramd1b 32
  • 90.5 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GRAMD1B 33
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GRAMD1B 33
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves GRAMD1B 33 32
  • 81.23 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GRAMD1B 33
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gramd1b 32
  • 73.31 (n)
zebrafish
(Danio rerio)
Actinopterygii GRAMD1B (1 of 2) 33
  • 75 (a)
OneToMany
gramd1b 32
  • 72.21 (n)
GRAMD1B (2 of 2) 33
  • 62 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG30284 33
  • 23 (a)
ManyToMany
CG34394 33
  • 20 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea ZC328.3 33
  • 24 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 33
  • 11 (a)
ManyToMany
YSP2 33
  • 10 (a)
ManyToMany
Species where no ortholog for GRAMD1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GRAMD1B Gene

ENSEMBL:
Gene Tree for GRAMD1B (if available)
TreeFam:
Gene Tree for GRAMD1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GRAMD1B: view image

Paralogs for GRAMD1B Gene

Paralogs for GRAMD1B Gene

(2) SIMAP similar genes for GRAMD1B Gene using alignment to 4 proteins:

  • GRM1B_HUMAN
  • E7EPH8_HUMAN
  • E9PRD6_HUMAN
  • J3KNL5_HUMAN
genes like me logo Genes that share paralogs with GRAMD1B: view

Variants for GRAMD1B Gene

Sequence variations from dbSNP and Humsavar for GRAMD1B Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000022240 -- 123,448,531(+) T/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000028651 -- 123,380,500(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000048949 -- 123,526,386(+) GGGGG/GGGG genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000053200 -- 123,448,238(+) C/A/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000054617 -- 123,508,520(+) A/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for GRAMD1B Gene

Variant ID Type Subtype PubMed ID
esv1010432 CNV deletion 20482838
esv2603228 CNV insertion 19546169
esv2663701 CNV deletion 23128226
esv2759868 CNV loss 17122850
esv3449847 CNV duplication 20981092
nsv513339 CNV insertion 21212237
nsv528 CNV insertion 18451855
nsv556483 CNV gain 21841781
nsv972081 CNV duplication 23825009

Variation tolerance for GRAMD1B Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.02; 37.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GRAMD1B Gene

Human Gene Mutation Database (HGMD)
GRAMD1B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GRAMD1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GRAMD1B Gene

Disorders for GRAMD1B Gene

Additional Disease Information for GRAMD1B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for GRAMD1B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GRAMD1B Gene

Publications for GRAMD1B Gene

  1. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10574462) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 56
  2. Aster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian Cells. (PMID: 30220461) Sandhu J … Tontonoz P (Cell 2018) 3 4 56
  3. Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. (PMID: 20731705) Lan Q … Rothman N (European journal of haematology 2010) 3 43 56
  4. Genetic susceptibility variants for chronic lymphocytic leukemia. (PMID: 20332261) Slager SL … Cerhan JR (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2010) 3 43 56
  5. A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia. (PMID: 18758461) Di Bernardo MC … Houlston RS (Nature genetics 2008) 3 43 56

Products for GRAMD1B Gene

Sources for GRAMD1B Gene