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

Gene ID: 57102, updated on 5-Mar-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
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Genomic context

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Location:
12p13.32
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (4487735..4538469, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (4494524..4545256, complement)
105.20220307 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
  • 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. 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
  3. Identification of C12orf4 as a gene for autosomal recessive intellectual disability. Philips AK, et al. Clin Genet, 2017 Jan. PMID 27311568
  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. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Alazami AM, et al. Cell Rep, 2015 Jan 13. PMID 25558065

See all (16) 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
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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
  

General protein information

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Preferred 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  protein C12orf4 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  protein C12orf4 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  protein C12orf4 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  protein C12orf4 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  protein C12orf4 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  protein C12orf4 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  protein C12orf4 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_2023_10

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  protein C12orf4 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  protein C12orf4 isoform X1

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

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