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GDAP2 ganglioside induced differentiation associated protein 2 [ Homo sapiens (human) ]

Gene ID: 54834, updated on 5-Mar-2024

Summary

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Official Symbol
GDAP2provided by HGNC
Official Full Name
ganglioside induced differentiation associated protein 2provided by HGNC
Primary source
HGNC:HGNC:18010
See related
Ensembl:ENSG00000196505 MIM:618128; AllianceGenome:HGNC:18010
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
SCAR27; MACROD3
Summary
Predicted to act upstream of or within response to retinoic acid. Located in lysosomal membrane. Implicated in autosomal recessive spinocerebellar ataxia 27. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 1.6), thyroid (RPKM 1.3) and 25 other tissues See more
Orthologs
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Genomic context

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See GDAP2 in Genome Data Viewer
Location:
1p12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (117863485..117929621, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (117872721..117938867, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (118406107..118472244, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene proline rich nuclear receptor coactivator 2 pseudogene 1 Neighboring gene uncharacterized LOC105378929 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:118380956-118382155 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:118385371-118386036 Neighboring gene Sharpr-MPRA regulatory region 13757 Neighboring gene WD repeat domain 3 Neighboring gene sperm associated antigen 17 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:118546660-118547175 Neighboring gene uncharacterized LOC105378930

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
  • 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. Isolation of 10 differentially expressed cDNAs in differentiated Neuro2a cells induced through controlled expression of the GD3 synthase gene. Liu H, et al. J Neurochem, 1999 May. PMID 10217254
  2. Hereditary Ataxia Overview. Adam MP, et al. , 1993. PMID 20301317
  3. A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase. Low TY, et al. Sci Signal, 2014 Dec 16. PMID 25515538
  4. Integral and associated lysosomal membrane proteins. Schröder B, et al. Traffic, 2007 Dec. PMID 17897319
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Boldt K, et al. Nat Commun, 2016 May 13. PMID 27173435, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

Associated conditions

Description Tests
Spinocerebellar ataxia, autosomal recessive 27
MedGen: C5193058 OMIM: 618369 GeneReviews: Not available
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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

  • FLJ20142, dJ776P7.1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in response to retinoic acid IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in lysosomal membrane HDA PubMed 

General protein information

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Preferred Names
ganglioside-induced differentiation-associated protein 2

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_001135589.3 → NP_001129061.1  ganglioside-induced differentiation-associated protein 2 isoform b

    See identical proteins and their annotated locations for NP_001129061.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains a 3' terminal exon that extends past a splice site, compared to variant 1. It encodes isoform b which is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AI125031, BC013132, BX100817, DB043931
    Consensus CDS
    CCDS44201.1
    UniProtKB/Swiss-Prot
    Q9NXN4
    Related
    ENSP00000358450.3, ENST00000369442.3
    Conserved Domains (2) summary
    cd02905
    Location:54 → 193
    Macro_GDAP2_like; Macro domain, GDAP2_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
    pfam13716
    Location:349 → 470
    CRAL_TRIO_2; Divergent CRAL/TRIO domain

  2. NM_017686.4 → NP_060156.1  ganglioside-induced differentiation-associated protein 2 isoform a

    See identical proteins and their annotated locations for NP_060156.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AA825512, AK000149, AL122007, BJ992034, BX459360, DB043931
    Consensus CDS
    CCDS897.1
    UniProtKB/Swiss-Prot
    Q96DZ0, Q9NXN4
    Related
    ENSP00000358451.4, ENST00000369443.10
    Conserved Domains (2) summary
    cd02905
    Location:54 → 193
    Macro_GDAP2_like; Macro domain, GDAP2_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
    pfam13716
    Location:349 → 480
    CRAL_TRIO_2; Divergent CRAL/TRIO domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    117863485..117929621 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    117872721..117938867 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXN4.1 GenPept UniProtKB/Swiss-Prot:Q9NXN4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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