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    FERRY3 FERRY endosomal RAB5 effector complex subunit 3 [ Homo sapiens (human) ]

    Gene ID: 57102, updated on 2-Nov-2024

    Summary

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    Official Symbol
    FERRY3provided by HGNC
    Official Full Name
    FERRY endosomal RAB5 effector complex subunit 3provided by HGNC
    Primary source
    HGNC:HGNC:1184
    See related
    Ensembl:ENSG00000047621 MIM:616082; AllianceGenome:HGNC:1184
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Fy-3; MRT66; C12orf4
    Summary
    This gene is highly conserved from nematodes to humans. In rat, the orthologous gene encodes a cytoplasmic protein that is involved in mast cell degranulation. The human gene has been implicated in autosomal recessive intellectual disability. [provided by RefSeq, Sep 2016]
    Expression
    Ubiquitous expression in brain (RPKM 4.7), thyroid (RPKM 4.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FERRY3 in Genome Data Viewer
    Location:
    12p13.32
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (4487735..4538469, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (4494524..4545256, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (4596901..4647635, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12719 Neighboring gene fibroblast growth factor 23 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4549412-4550163 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4550164-4550914 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4550915-4551665 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4559670-4560372 Neighboring gene fibroblast growth factor 6 Neighboring gene Sharpr-MPRA regulatory region 2870 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4618390-4619024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5825 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:4647270-4647879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:4647880-4648488 Neighboring gene RAD51 associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 10040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5826 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 4 Neighboring gene coiled-coil domain containing 181 pseudogene

    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. A novel variant of C12orf4 linked to autosomal recessive intellectual disability type 66 with phenotype expansion. Rashvand Z, et al. J Gene Med, 2022 Apr. PMID 34967075
    2. Identification of C12orf4 as a gene for autosomal recessive intellectual disability. Philips AK, et al. Clin Genet, 2017 Jan. PMID 27311568
    3. A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. Dudkiewicz M, et al. PeerJ, 2019. PMID 31106069, Free PMC Article
    4. In-cell intrabody selection from a diverse human library identifies C12orf4 protein as a new player in rodent mast cell degranulation. Mazuc E, et al. PLoS One, 2014. PMID 25122211, Free PMC Article
    5. The Rab5 effector FERRY links early endosomes with mRNA localization. Schuhmacher JS, et al. Mol Cell, 2023 Jun 1. PMID 37267905

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel variant of C12orf4 linked to autosomal recessive intellectual disability type 66 with phenotype expansion.
      Title: A novel variant of C12orf4 linked to autosomal recessive intellectual disability type 66 with phenotype expansion.
    2. Results indicate a founder missense variant (p.Leu328Pro) in seven affected individuals from two Finnish consanguineous families and a deletion (p.Gln267fs) in one affected individual from a consanguineous Dutch family in the C12orf4 gene on chromosome 12.
      Title: Identification of C12orf4 as a gene for autosomal recessive intellectual disability.
    3. Mass spectrometry analysis identified protein RGD1311164 (C12orf4), with no previously described function. Our data demonstrate that RGD1311164 is a cytoplasmic protein implicated in the early signaling events following FcepsilonRI-induced cell activation
      Title: In-cell intrabody selection from a diverse human library identifies C12orf4 protein as a new player in rodent mast cell degranulation.
    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
    Intellectual disability, autosomal recessive 66
    MedGen: C4748732 OMIM: 618221 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Common genetic variants associate with serum phosphorus concentration.
    EBI GWAS Catalog

    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

    • FLJ21158, FLJ23899

    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 regulation of mast cell degranulation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mast cell degranulation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ferry endosomal RAB5 effector complex subunit 3
    Names
    protein C12orf4

    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.

    Genomic

    1. NG_051648.1 RefSeqGene

      Range
      5040..55774
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001304811.2 → NP_001291740.1  ferry endosomal RAB5 effector complex subunit 3 isoform a

      See identical proteins and their annotated locations for NP_001291740.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK074479, AL834377, BM556376, DA195770, R59546
      Consensus CDS
      CCDS8528.1
      UniProtKB/Swiss-Prot
      D3DUQ8, Q6MZH5, Q9NQ89
      Related
      ENSP00000439996.1, ENST00000545746.5
      Conserved Domains (1) summary
      pfam10154
      Location:41 → 546
      DUF2362; Uncharacterized conserved protein (DUF2362)

    2. NM_001346153.2 → NP_001333082.1  ferry endosomal RAB5 effector complex subunit 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
      Source sequence(s)
      AC005832, AC008012, AC092826

    3. NM_001346155.2 → NP_001333084.1  ferry endosomal RAB5 effector complex subunit 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 3 and 4 both encode the same isoform (b).
      Source sequence(s)
      AC005832, AC008012, AC092826

    4. NM_001346156.2 → NP_001333085.1  ferry endosomal RAB5 effector complex subunit 3 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC005832, AC008012, AC092826
      Conserved Domains (1) summary
      pfam10154
      Location:1 → 373
      DUF2362; Uncharacterized conserved protein (DUF2362)

    5. NM_001346157.2 → NP_001333086.1  ferry endosomal RAB5 effector complex subunit 3 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks an in-frame exon compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC005832, AC008012, AC092826
      Conserved Domains (1) summary
      pfam10154
      Location:1 → 330
      DUF2362; Uncharacterized conserved protein (DUF2362)

    6. NM_001352962.2 → NP_001339891.1  ferry endosomal RAB5 effector complex subunit 3 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC005832, AC008012, AC092826
      Conserved Domains (1) summary
      pfam10154
      Location:1 → 262
      DUF2362; Uncharacterized conserved protein (DUF2362)

    7. NM_020374.4 → NP_065107.1  ferry endosomal RAB5 effector complex subunit 3 isoform a

      See identical proteins and their annotated locations for NP_065107.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK074479, AL834377, BM556376, R59546
      Consensus CDS
      CCDS8528.1
      UniProtKB/Swiss-Prot
      D3DUQ8, Q6MZH5, Q9NQ89
      Related
      ENSP00000261250.3, ENST00000261250.8
      Conserved Domains (1) summary
      pfam10154
      Location:41 → 546
      DUF2362; Uncharacterized conserved protein (DUF2362)

    RNA

    1. NR_144379.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC005832, AC008012, AC092826

    2. NR_144380.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks three alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC005832, AC008012, AC092826

    3. NR_144382.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) lacks four alternate exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC005832, AC008012, AC092826

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      4487735..4538469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006718992.4 → XP_006719055.1  ferry endosomal RAB5 effector complex subunit 3 isoform X1

      Conserved Domains (1) summary
      pfam10154
      Location:41 → 410
      DUF2362; Uncharacterized conserved protein (DUF2362)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      4494524..4545256 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372607.1 → XP_054228582.1  ferry endosomal RAB5 effector complex subunit 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQ89.1 GenPept UniProtKB/Swiss-Prot:Q9NQ89

    Gene LinkOut

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

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