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

Summary

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, Dec 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

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S425 (e-PCR), detects polymorphism
- UniSTS:29716

D19S425 (e-PCR), detects polymorphism
- UniSTS:24090

D19S425 (e-PCR), detects polymorphism
- UniSTS:24186

A004D32 (e-PCR)
- UniSTS:17809

D19S569 (e-PCR)
- UniSTS:80044

SHGC-151016 (e-PCR)
- UniSTS:173502

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)

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)
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)
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)
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)
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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

34994727..35026469

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B3KUH3
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)
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)
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)
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)
XM_047439134.1 → XP_047295090.1 protein Aster-A isoform X7

UniProtKB/TrEMBL

B3KQF7

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

37539338..37571085

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B3KUH3
XM_054321550.1 → XP_054177525.1 protein Aster-A isoform X9

UniProtKB/TrEMBL

B3KUH3
XM_054321548.1 → XP_054177523.1 protein Aster-A isoform X3

UniProtKB/TrEMBL

B3KUH3
XM_054321547.1 → XP_054177522.1 protein Aster-A isoform X8

UniProtKB/TrEMBL

B3KUH3
XM_054321556.1 → XP_054177531.1 protein Aster-A isoform X10
XM_054321552.1 → XP_054177527.1 protein Aster-A isoform X5

UniProtKB/TrEMBL

B3KUH3
XM_054321554.1 → XP_054177529.1 protein Aster-A isoform X6

UniProtKB/TrEMBL

B3KUH3
XM_054321551.1 → XP_054177526.1 protein Aster-A isoform X5

UniProtKB/TrEMBL

B3KUH3
XM_054321553.1 → XP_054177528.1 protein Aster-A isoform X6

UniProtKB/TrEMBL

B3KUH3
XM_054321555.1 → XP_054177530.1 protein Aster-A isoform X7

UniProtKB/TrEMBL

B3KQF7