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    GARIN1B golgi associated RAB2 interactor 1B [ Homo sapiens (human) ]

    Gene ID: 84691, updated on 28-Oct-2024

    Summary

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    Official Symbol
    GARIN1Bprovided by HGNC
    Official Full Name
    golgi associated RAB2 interactor 1Bprovided by HGNC
    Primary source
    HGNC:HGNC:30704
    See related
    Ensembl:ENSG00000135248 MIM:619905; AllianceGenome:HGNC:30704
    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
    GARIL1; FAM137A; FAM71F1; GARI-L1; NYD-SP18
    Summary
    Predicted to be involved in acrosome assembly and acrosome reaction. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Restricted expression toward testis (RPKM 24.4) See more
    Orthologs
    mouse all
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    Genomic context

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    See GARIN1B in Genome Data Viewer
    Location:
    7q32.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (128709061..128731743)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130021222..130043893)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128349115..128371797)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene golgi associated RAB2 interactor 1A Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:128341516-128342715 Neighboring gene RNA, 5S ribosomal pseudogene 242 Neighboring gene RNA, 5S ribosomal pseudogene 243 Neighboring gene uncharacterized LOC124901825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26603 Neighboring gene calumenin Neighboring gene RNA, 7SL, cytoplasmic 81, pseudogene Neighboring gene blue cone (S) opsin upstream regulatory region Neighboring gene opsin 1, short wave sensitive

    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. Lack of Association between NYD-SP18 Variant and Obesity. The Health Alcohol and Psychosocial Factors in Eastern Europe Study. Hubacek JA, et al. Ann Nutr Metab, 2016. PMID 27237450, Free PMC Article
    2. Body Composition Changes in Adult Females after Lifestyle Intervention Are Influenced by the NYD-SP18 Variant. Suchánek P, et al. Cent Eur J Public Health, 2015 Nov. PMID 26849538
    3. NYD-SP18 is associated with obesity in the NHLBI Family Heart Study. Wilk JB, et al. Int J Obes (Lond), 2008 Jun. PMID 18317470, Free PMC Article
    4. Body Adiposity Changes After Lifestyle Interventions in Children/Adolescents and the NYD-SP18 and TMEM18 Variants. Zlatohlavek L, et al. Med Sci Monit, 2018 Oct 20. PMID 30341978, Free PMC Article
    5. Strong gender-specific additive effects of the NYD-SP18 and FTO variants on BMI values. Hubacek JA, et al. Physiol Res, 2015. PMID 26680676

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Decreased body weight in overweight/obese children is not significantly influenced by the NYD-SP18 rs6971091 or TMEM18 rs4854344 polymorphisms. Gene Indexing Project Expand All Collapse All Decreased body weight in overweight/obese children is not significantly influenced by the NYD-SP18 rs6971091 or TMEM18 rs4854344 polymorphisms.
      Title: Body Adiposity Changes After Lifestyle Interventions in Children/Adolescents and the NYD-SP18 and TMEM18 Variants.
    2. genetic association studies in populations in Eastern Europe (Czech Republic, Lithuania, Poland, and Russia): Data suggest that an SNP in NYD-SP18 (rs6971091) is not associated with overweight/obesity in the adult populations studied (aged 45-75).
      Title: Lack of Association between NYD-SP18 Variant and Obesity. The Health Alcohol and Psychosocial Factors in Eastern Europe Study.
    3. Genetic variants within NYD-SP18 genes revealed a significant additive effect on BMI values in males.
      Title: Strong gender-specific additive effects of the NYD-SP18 and FTO variants on BMI values.
    4. Overweight/obese female carriers of the NYD-SP18 rs6971091 GG genotype exhibited a more beneficial response to the intensive lifestyle intervention than others.
      Title: Body Composition Changes in Adult Females after Lifestyle Intervention Are Influenced by the NYD-SP18 Variant.
    5. The effect of the NYD-SP18 SNP on obesity was larger than the effect of FTO in FHS. The NYD-SP18 gene is described as testes development related, but little is known about the gene's function or the mechanism by which it may influence risk for obesity.
      Title: NYD-SP18 is associated with obesity in the NHLBI Family Heart Study.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: NYD-SP18 is associated with obesity in the NHLBI Family Heart Study.
    Submit: New GeneRIF Correction

    Phenotypes

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    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

    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 acrosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in acrosome reaction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    Golgi-associated RAB2 interactor protein 1B
    Names
    Golgi associated RAB2 interactor protein 1B
    Golgi-associated RAB2B interactor like 1
    family with sequence similarity 137, member A
    family with sequence similarity 71 member F1
    protein FAM71F1
    testes development-related NYD-SP18
    testicular tissue protein Li 67
    testis development protein NYD-SP18

    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_001282788.3 → NP_001269717.1  Golgi-associated RAB2 interactor protein 1B isoform 2

      See identical proteins and their annotated locations for NP_001269717.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the 3' coding region compared to variant 1. The resulting isoform (2) is 2 aa shorter than isoform 1.
      Source sequence(s)
      AC018638, AC024952
      Consensus CDS
      CCDS94192.1
      UniProtKB/Swiss-Prot
      Q96KD3
      Related
      ENSP00000477573.2, ENST00000621392.5
      Conserved Domains (1) summary
      pfam12480
      Location:140 → 208
      DUF3699; Protein of unknown function (DUF3699)

    2. NM_001282789.2 → NP_001269718.1  Golgi-associated RAB2 interactor protein 1B isoform 3

      See identical proteins and their annotated locations for NP_001269718.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains 2 alternate exons at the 5' end and uses 2 alternate in-frame acceptor splice sites compared to variant 1. The former difference results in translation initiation from an upstream start codon and a shorter isoform (3) with a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK093161, AK302221, BC032842
      Consensus CDS
      CCDS64763.1
      UniProtKB/Swiss-Prot
      Q96KD3
      UniProtKB/TrEMBL
      B4DY15
      Related
      ENSP00000418192.1, ENST00000485070.5
      Conserved Domains (1) summary
      pfam12480
      Location:36 → 109
      DUF3699; Protein of unknown function (DUF3699)

    3. NM_032599.4 → NP_115988.1  Golgi-associated RAB2 interactor protein 1B isoform 1

      See identical proteins and their annotated locations for NP_115988.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF367470, BC032842, HY051242
      Consensus CDS
      CCDS5804.1
      UniProtKB/Swiss-Prot
      Q8IY75, Q8NA48, Q96KD3
      UniProtKB/TrEMBL
      A0A140VJJ3
      Related
      ENSP00000326652.4, ENST00000315184.9
      Conserved Domains (1) summary
      pfam12480
      Location:138 → 208
      DUF3699; Protein of unknown function (DUF3699)

    RNA

    1. NR_104242.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an additional internal exon and uses an alternate acceptor splice site compared to variant 1. This variant is represented as non-coding because use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK310308, BC032842, HY051242

    2. NR_104243.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains several differences, including 2 exons at the 5' end and an internal exon, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translation start codon renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK302221, AK310308, BC032842, BC040906
      Related
      ENST00000484425.6

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      128709061..128731743
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420990.1 → XP_047276946.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    2. XM_047420991.1 → XP_047276947.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    3. XM_047420987.1 → XP_047276943.1  Golgi-associated RAB2 interactor protein 1B isoform X1

    4. XM_047420988.1 → XP_047276944.1  Golgi-associated RAB2 interactor protein 1B isoform X2

    5. XM_047420989.1 → XP_047276945.1  Golgi-associated RAB2 interactor protein 1B isoform X3

      Related
      ENSP00000418672.1, ENST00000471558.5

    6. XM_047420992.1 → XP_047276948.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    RNA

    1. XR_007060168.1 RNA Sequence

    2. XR_007060169.1 RNA Sequence

    3. XR_007060170.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      130021222..130043893
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359268.1 → XP_054215243.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    2. XM_054359269.1 → XP_054215244.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    3. XM_054359267.1 → XP_054215242.1  Golgi-associated RAB2 interactor protein 1B isoform X3

    4. XM_054359265.1 → XP_054215240.1  Golgi-associated RAB2 interactor protein 1B isoform X1

    5. XM_054359266.1 → XP_054215241.1  Golgi-associated RAB2 interactor protein 1B isoform X2

    6. XM_054359270.1 → XP_054215245.1  Golgi-associated RAB2 interactor protein 1B isoform X4

    RNA

    1. XR_008487766.1 RNA Sequence

    2. XR_008487767.1 RNA Sequence

    3. XR_008487768.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96KD3.1 GenPept UniProtKB/Swiss-Prot:Q96KD3

    Gene LinkOut

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

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