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C12orf4 chromosome 12 open reading frame 4 [ Homo sapiens (human) ]

Gene ID: 57102, updated on 20-Dec-2019

Summary

Official Symbol
C12orf4provided by HGNC
Official Full Name
chromosome 12 open reading frame 4provided by HGNC
Primary source
HGNC:HGNC:1184
See related
Ensembl:ENSG00000047621 MIM:616082
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
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

Genomic context

See C12orf4 in Genome Data Viewer
Location:
12p13.32
Exon count:
15
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (4487730..4538508, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (4596899..4647674, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene fibroblast growth factor 6 Neighboring gene Sharpr-MPRA regulatory region 2870 Neighboring gene RAD51 associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 10040 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 4

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 66
MedGen: C4748732 OMIM: 618221 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
Common genetic variants associate with serum phosphorus concentration.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21158, FLJ23899

Gene Ontology Provided by GOA

Process Evidence Code Pubs
regulation of mast cell degranulation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 

NCBI Reference Sequences (RefSeq)

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_001304811.1NP_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
    Q9NQ89
    Related
    ENSP00000439996.1, ENST00000545746.5
    Conserved Domains (1) summary
    pfam10154
    Location:41546
    DUF2362; Uncharacterized conserved protein (DUF2362)
  2. NM_001346153.1NP_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_001346155.1NP_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_001346156.1NP_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:1373
    DUF2362; Uncharacterized conserved protein (DUF2362)
  5. NM_001346157.1NP_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:1330
    DUF2362; Uncharacterized conserved protein (DUF2362)
  6. NM_001352962.1NP_001339891.1  protein C12orf4 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC005832, AC008012, AC092826
    Conserved Domains (1) summary
    pfam10154
    Location:1262
    DUF2362; Uncharacterized conserved protein (DUF2362)
  7. NM_020374.4NP_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
    Q9NQ89
    Related
    ENSP00000261250.3, ENST00000261250.8
    Conserved Domains (1) summary
    pfam10154
    Location:41546
    DUF2362; Uncharacterized conserved protein (DUF2362)

RNA

  1. NR_144379.1 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_144380.1 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_144382.1 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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    4487730..4538508 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718992.3XP_006719055.1  protein C12orf4 isoform X1

    Conserved Domains (1) summary
    pfam10154
    Location:41410
    DUF2362; Uncharacterized conserved protein (DUF2362)
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