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

Gene ID: 84691, updated on 3-Apr-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
Expression
Restricted expression toward testis (RPKM 24.4) See more
Orthologs
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Genomic context

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Location:
7q32.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (128709061..128731743)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130021222..130043893)
105.20220307 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
  • 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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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

Gene Ontology Provided by GOA

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_2023_10

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

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