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] See more...

Aliases for C12orf4 Gene

Aliases for C12orf4 Gene

  • Chromosome 12 Open Reading Frame 4 2 3 5
  • Protein C12orf4 3 4

External Ids for C12orf4 Gene

Previous GeneCards Identifiers for C12orf4 Gene

  • GC12M004336
  • GC12M004489
  • GC12M004596

Summaries for C12orf4 Gene

Entrez Gene Summary for C12orf4 Gene

  • 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]

GeneCards Summary for C12orf4 Gene

C12orf4 (Chromosome 12 Open Reading Frame 4) is a Protein Coding gene. Diseases associated with C12orf4 include Mental Retardation, Autosomal Recessive 66 and Attention Deficit-Hyperactivity Disorder.

UniProtKB/Swiss-Prot Summary for C12orf4 Gene

Additional gene information for C12orf4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for C12orf4 Gene

Genomics for C12orf4 Gene

GeneHancer (GH) Regulatory Elements for C12orf4 Gene

Promoters and enhancers for C12orf4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J004537 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 -0.3 -293 3.6 FOXK2 ZBTB40 ZNF217 EP300 SIN3A NRF1 TCF12 POLR2G USF1 SP1 C12orf4 RAD51AP1 lnc-C12orf4-1 HSALNG0088727
GH12J004561 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10.6 -23.7 -23680 1.2 NRF1 TEAD4 ZIC2 ZBTB26 REST RFX1 MYC HDAC2 ZNF341 ZSCAN9 DYRK4 lnc-RAD51AP1-1 C12orf4 RAD51AP1 AKAP3 HSALNG0088727
GH12J004439 Enhancer 0.9 ENCODE CraniofacialAtlas 14.5 +97.3 97253 2.9 ZIC2 OSR2 ZBTB17 ZFHX2 ZNF335 ZBTB48 IKZF3 KLF17 ZNF843 EZH2 C12orf4 FGF23 RAD51AP1 FGF6 piR-48373-003
GH12J004568 Promoter/Enhancer 1 Ensembl ENCODE 11.8 -29.4 -29393 2.6 SRF NBN SPI1 ELF1 NR2F1 IKZF1 BHLHE40 NR2F6 MTA2 IKZF2 AKAP3 C12orf4 RAD51AP1 ENSG00000256748 NDUFA9 TIGAR lnc-RAD51AP1-1 DYRK4 piR-48209-101
GH12J005051 Enhancer 0.9 Ensembl dbSUPER 10.4 -514.2 -514193 3.4 EP300 ZNF623 ZBTB11 ZNF426 ZNF213 IRF4 IKZF1 ZNF654 ZFP64 ZNF34 C12orf4 DYRK4 KCNA1 HSALNG0088768 ENSG00000285523
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C12orf4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for C12orf4

Top Transcription factor binding sites by QIAGEN in the C12orf4 gene promoter:
  • AREB6
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • PPAR-gamma1
  • PPAR-gamma2
  • RORalpha2

Genomic Locations for C12orf4 Gene

Genomic Locations for C12orf4 Gene
chr12:4,487,730-4,538,508
(GRCh38/hg38)
Size:
50,779 bases
Orientation:
Minus strand
chr12:4,596,894-4,647,674
(GRCh37/hg19)
Size:
50,781 bases
Orientation:
Minus strand

Genomic View for C12orf4 Gene

Genes around C12orf4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C12orf4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C12orf4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C12orf4 Gene

Proteins for C12orf4 Gene

  • Protein details for C12orf4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQ89-CL004_HUMAN
    Recommended name:
    Protein C12orf4
    Protein Accession:
    Q9NQ89
    Secondary Accessions:
    • D3DUQ8
    • Q6MZH5

    Protein attributes for C12orf4 Gene

    Size:
    552 amino acids
    Molecular mass:
    63801 Da
    Quaternary structure:
    No Data Available

neXtProt entry for C12orf4 Gene

Post-translational modifications for C12orf4 Gene

  • Ubiquitination at Lys220
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for C12orf4 Gene

Domains & Families for C12orf4 Gene

Gene Families for C12orf4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for C12orf4 Gene

InterPro:
ProtoNet:
genes like me logo Genes that share domains with C12orf4: view

No data available for Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for C12orf4 Gene

Function for C12orf4 Gene

Molecular function for C12orf4 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in mast cell degranulation.

Phenotypes From GWAS Catalog for C12orf4 Gene

genes like me logo Genes that share phenotypes with C12orf4: view

Human Phenotype Ontology for C12orf4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for C12orf4 Gene

MGI Knock Outs for C12orf4:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for C12orf4 Gene

Localization for C12orf4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C12orf4 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for C12orf4 gene
Compartment Confidence
nucleus 1
cytosol 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for C12orf4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm ISS --
genes like me logo Genes that share ontologies with C12orf4: view

Pathways & Interactions for C12orf4 Gene

PathCards logo

SuperPathways for C12orf4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for C12orf4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043304 regulation of mast cell degranulation ISS --
genes like me logo Genes that share ontologies with C12orf4: view

No data available for Pathways by source and SIGNOR curated interactions for C12orf4 Gene

Drugs & Compounds for C12orf4 Gene

No Compound Related Data Available

Transcripts for C12orf4 Gene

mRNA/cDNA for C12orf4 Gene

7 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C12orf4 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: -
SP2:

Relevant External Links for C12orf4 Gene

GeneLoc Exon Structure for
C12orf4

Expression for C12orf4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C12orf4 Gene

Protein differential expression in normal tissues from HIPED for C12orf4 Gene

This gene is overexpressed in Pancreatic juice (10.6), Placenta (7.5), Fetal Brain (7.5), Peripheral blood mononuclear cells (6.0), and Testis (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C12orf4 Gene



Protein tissue co-expression partners for C12orf4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C12orf4

SOURCE GeneReport for Unigene cluster for C12orf4 Gene:

Hs.302977

Evidence on tissue expression from TISSUES for C12orf4 Gene

  • Eye(4.1)
  • Liver(4.1)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with C12orf4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for C12orf4 Gene

Orthologs for C12orf4 Gene

This gene was present in the common ancestor of animals.

Orthologs for C12orf4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C12orf4 31
  • 100 (a)
OneToOne
C12H12orf4 30
  • 99.64 (n)
dog
(Canis familiaris)
Mammalia C12orf4 31
  • 97 (a)
OneToOne
C27H12orf4 30
  • 93.18 (n)
cow
(Bos Taurus)
Mammalia C5H12ORF4 31 31
  • 96 (a)
OneToMany
C5H12orf4 30
  • 88.1 (n)
oppossum
(Monodelphis domestica)
Mammalia C12orf4 31
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia RGD1311164 30
  • 86.9 (n)
mouse
(Mus musculus)
Mammalia D6Wsu163e 17 31 30
  • 86.23 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia C12orf4 31
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves C1H12ORF4 31 30
  • 79.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C12orf4 31
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia c12orf4 30
  • 70.92 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC53313 30
zebrafish
(Danio rerio)
Actinopterygii C25H12orf4 31
  • 78 (a)
OneToOne
zgc:154077 30
  • 69.39 (n)
Dr.19005 30
fruit fly
(Drosophila melanogaster)
Insecta CG9986 31 32 30
  • 47.35 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004141 30
  • 45 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C55A6.10 30
  • 44.44 (n)
C55A6.10 31 32
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 37 (a)
OneToOne
Cin.5648 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5648 30
Species where no ortholog for C12orf4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for C12orf4 Gene

ENSEMBL:
Gene Tree for C12orf4 (if available)
TreeFam:
Gene Tree for C12orf4 (if available)

Paralogs for C12orf4 Gene

No data available for Paralogs for C12orf4 Gene

Variants for C12orf4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for C12orf4 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
717449 Likely Benign: not provided 4,490,514(-) T/C INTRON_VARIANT
723335 Benign: not provided 4,517,141(-) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
736588 Likely Benign: not provided 4,529,928(-) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
rs1468772495 Pathogenic: MENTAL RETARDATION, AUTOSOMAL RECESSIVE 66. Mental retardation, autosomal recessive 66 (MRT66) [MIM:618221] 4,518,108(-) A/Gp.Leu328Pro MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs730882197 Pathogenic/Likely Pathogenic: Intellectual disability; Muscular hypotonia; Attention deficit hyperactivity disorder; MENTAL RETARDATION, AUTOSOMAL RECESSIVE 66 4,525,342(-) G/GTTGT FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for C12orf4 Gene

Structural Variations from Database of Genomic Variants (DGV) for C12orf4 Gene

Variant ID Type Subtype PubMed ID
nsv1040098 CNV gain 25217958
nsv1139563 CNV duplication 24896259
nsv483060 CNV loss 15286789
nsv557123 CNV gain 21841781
nsv586 CNV insertion 18451855

Variation tolerance for C12orf4 Gene

Residual Variation Intolerance Score: 10.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C12orf4 Gene

Human Gene Mutation Database (HGMD)
C12orf4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
C12orf4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C12orf4 Gene

Disorders for C12orf4 Gene

MalaCards: The human disease database

(5) MalaCards diseases for C12orf4 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CL004_HUMAN
  • Mental retardation, autosomal recessive 66 (MRT66) [MIM:618221]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT66 patients have intellectual disability, delayed speech development, neuropsychiatric symptoms, and relatively normal life span. {ECO:0000269 PubMed:25558065, ECO:0000269 PubMed:27311568, ECO:0000269 PubMed:28097321}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for C12orf4

genes like me logo Genes that share disorders with C12orf4: view

No data available for Genatlas for C12orf4 Gene

Publications for C12orf4 Gene

  1. Identification of C12orf4 as a gene for autosomal recessive intellectual disability. (PMID: 27311568) Philips AK … Järvelä I (Clinical genetics 2017) 2 3 4 54
  2. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. (PMID: 25558065) Alazami AM … Alkuraya FS (Cell reports 2015) 2 3 4 54
  3. In-cell intrabody selection from a diverse human library identifies C12orf4 protein as a new player in rodent mast cell degranulation. (PMID: 25122211) Mazuc E … Martineau P (PloS one 2014) 2 3 54
  4. Common genetic variants associate with serum phosphorus concentration. (PMID: 20558539) Kestenbaum B … Fox CS (Journal of the American Society of Nephrology : JASN 2010) 3 41 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for C12orf4 Gene

Sources for C12orf4 Gene