Aliases for PTCHD4 Gene

Aliases for PTCHD4 Gene

  • Patched Domain Containing 4 2 3 5
  • PTCH53 2 3 4
  • Patched Domain-Containing Protein 4 3 4
  • P53-Regulated Patched Protein 3 4
  • DJ402H5.2 2 3
  • C6orf138 3 4
  • Patched Domain-Containing Protein C6orf138 3
  • Chromosome 6 Open Reading Frame 138 2
  • FLJ41841 2
  • PTCHD4 5

External Ids for PTCHD4 Gene

Previous HGNC Symbols for PTCHD4 Gene

  • C6orf138

Summaries for PTCHD4 Gene

GeneCards Summary for PTCHD4 Gene

PTCHD4 (Patched Domain Containing 4) is a Protein Coding gene. Diseases associated with PTCHD4 include Otopalatodigital Syndrome, Type I and Basal Cell Nevus Syndrome. Gene Ontology (GO) annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is PTCHD1.

UniProtKB/Swiss-Prot Summary for PTCHD4 Gene

  • Could act as a repressor of canonical hedgehog signaling by antagonizing the effects of SMO, as suggested by down-regulation of hedgehog target genes, including GLI1, PTCH1, and PTCH2 in PTCHD4-expressing cells.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTCHD4 Gene

Genomics for PTCHD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTCHD4 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
GH06J048070 Promoter 1.6 UCNEbase EPDnew Ensembl CraniofacialAtlas 255.3 +42.3 42295 1.8 RBM22 RAD21 BACH1 PTCHD4 HSALNG0050440 HSALNG0050442 ENSG00000286811 OPN5
GH06J048109 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 255.4 +1.0 957 3.3 CEBPA THAP11 FOXA2 ZNF511 SMAD4 SAP130 MIER3 ETV4 TEAD3 DMAP1 PTCHD4 ENSG00000286811 piR-58308-286 HSALNG0050444 OPN5
GH06J047167 Enhancer 1.1 ENCODE dbSUPER 11 +941.9 941943 4 FEZF1 CEBPA DEK ZNF217 BRCA1 SIX4 ZIC2 ZNF610 CEBPB ZNF513 SLC25A27 TDRD6 PTCHD4 HSALNG0050395 lnc-MEP1A-5 LOC105375081 RF00017-5588 ADGRF1 TNFRSF21
GH06J048765 Enhancer 0.8 Ensembl ENCODE 11 -654.6 -654622 2.8 CTCF SIX4 CEBPB EP300 SMC3 RAD21 TBP JUND ZNF384 ARID3A PTCHD4 RNU1-105P CENPQ MMUT piR-39655-006 HSALNG0050465 ENSG00000287137
GH06J048037 Enhancer 0.6 FANTOM5 Ensembl 11.3 +73.4 73396 1.6 FOXA2 NFE2 NFE2L2 SPI1 PTCHD4 RNU1-105P piR-40110-592 HSALNG0050440 HSALNG0050438 OPN5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTCHD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTCHD4

Genomic Locations for PTCHD4 Gene

Latest Assembly
chr6:47,856,673-48,111,197
(GRCh38/hg38)
Size:
254,525 bases
Orientation:
Minus strand

Previous Assembly
chr6:47,824,409-48,078,933
(GRCh37/hg19 by Entrez Gene)
Size:
254,525 bases
Orientation:
Minus strand

chr6:47,845,764-48,036,425
(GRCh37/hg19 by Ensembl)
Size:
190,662 bases
Orientation:
Minus strand

Genomic View for PTCHD4 Gene

Genes around PTCHD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCHD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCHD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTCHD4 Gene

Proteins for PTCHD4 Gene

  • Protein details for PTCHD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZW05-PTHD4_HUMAN
    Recommended name:
    Patched domain-containing protein 4
    Protein Accession:
    Q6ZW05
    Secondary Accessions:
    • A0A0A7EN49
    • B0QZ29
    • B2RPC0
    • B4DRK3
    • B4DTR9
    • Q5T884

    Protein attributes for PTCHD4 Gene

    Size:
    846 amino acids
    Molecular mass:
    96371 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAI37360.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAI37365.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC85703.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC85703.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=EAX04325.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for PTCHD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTCHD4 Gene

Post-translational modifications for PTCHD4 Gene

  • Glycosylation at Asn762
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PTCHD4 Gene

Domains & Families for PTCHD4 Gene

Gene Families for PTCHD4 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PTCHD4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PTCHD4 Gene

GenScript: Design optimal peptide antigens:
  • C6orf138 protein (B2RPC0_HUMAN)
  • Patched domain-containing protein C6orf138 (CF138_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZW05

UniProtKB/Swiss-Prot:

PTHD4_HUMAN :
  • Belongs to the patched family.
Family:
  • Belongs to the patched family.
genes like me logo Genes that share domains with PTCHD4: view

Function for PTCHD4 Gene

Molecular function for PTCHD4 Gene

UniProtKB/Swiss-Prot Function:
Could act as a repressor of canonical hedgehog signaling by antagonizing the effects of SMO, as suggested by down-regulation of hedgehog target genes, including GLI1, PTCH1, and PTCH2 in PTCHD4-expressing cells.
UniProtKB/Swiss-Prot Induction:
Induced by TP53.

Phenotypes From GWAS Catalog for PTCHD4 Gene

Gene Ontology (GO) - Molecular Function for PTCHD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with PTCHD4: view
genes like me logo Genes that share phenotypes with PTCHD4: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCHD4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PTCHD4 Gene

Localization for PTCHD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCHD4 Gene

Membrane. Multi-pass membrane protein.

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 PTCHD4 gene
Compartment Confidence
plasma membrane 2
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PTCHD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0016020 membrane IEA,IBA 21873635
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PTCHD4: view

Pathways & Interactions for PTCHD4 Gene

PathCards logo

SuperPathways for PTCHD4 Gene

No Data Available

Interacting Proteins for PTCHD4 Gene

Gene Ontology (GO) - Biological Process for PTCHD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with PTCHD4: view

No data available for Pathways by source and SIGNOR curated interactions for PTCHD4 Gene

Drugs & Compounds for PTCHD4 Gene

No Compound Related Data Available

Transcripts for PTCHD4 Gene

mRNA/cDNA for PTCHD4 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCHD4

Alternative Splicing Database (ASD) splice patterns (SP) for PTCHD4 Gene

No ASD Table

Relevant External Links for PTCHD4 Gene

GeneLoc Exon Structure for
PTCHD4

Expression for PTCHD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTCHD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTCHD4 Gene



Protein tissue co-expression partners for PTCHD4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTCHD4

SOURCE GeneReport for Unigene cluster for PTCHD4 Gene:

Hs.659409

Evidence on tissue expression from TISSUES for PTCHD4 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with PTCHD4: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCHD4 Gene

Orthologs for PTCHD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTCHD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTCHD4 30 31
  • 99.08 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTCHD4 30 31
  • 95.47 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PTCHD4 31
  • 95 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptchd4 30
  • 92.87 (n)
Mouse
(Mus musculus)
Mammalia Ptchd4 30 17 31
  • 92.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia C23H6orf138 31
  • 92 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PTCHD4 31
  • 89 (a)
OneToOne
Chicken
(Gallus gallus)
Aves C3H6ORF138 30 31
  • 81.95 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTCHD4 31
  • 83 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptchd4 30
  • 74.57 (n)
Zebrafish
(Danio rerio)
Actinopterygii ptchd4 30 31
  • 71.27 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Ptr 31
  • 17 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ptr-10 31
  • 21 (a)
ManyToMany
ptr-2 31
  • 21 (a)
ManyToMany
ptr-15 31
  • 19 (a)
ManyToMany
ptr-9 31
  • 19 (a)
ManyToMany
daf-6 31
  • 19 (a)
ManyToMany
ptr-19 31
  • 18 (a)
ManyToMany
ptr-17 31
  • 17 (a)
ManyToMany
ptr-18 31
  • 17 (a)
ManyToMany
ptr-20 31
  • 16 (a)
ManyToMany
ptr-1 31
  • 16 (a)
ManyToMany
ptr-14 31
  • 16 (a)
ManyToMany
ptr-6 31
  • 16 (a)
ManyToMany
ptr-4 31
  • 16 (a)
ManyToMany
ptr-22 31
  • 16 (a)
ManyToMany
ptr-13 31
  • 16 (a)
ManyToMany
ptr-11 31
  • 15 (a)
ManyToMany
ptr-5 31
  • 14 (a)
ManyToMany
ptr-23 31
  • 14 (a)
ManyToMany
ptr-12 31
  • 14 (a)
ManyToMany
ptr-3 31
  • 14 (a)
ManyToMany
ptr-16 31
  • 14 (a)
ManyToMany
ptr-8 31
  • 14 (a)
ManyToMany
ptr-21 31
  • 14 (a)
ManyToMany
Species where no ortholog for PTCHD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 PTCHD4 Gene

ENSEMBL:
Gene Tree for PTCHD4 (if available)
TreeFam:
Gene Tree for PTCHD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTCHD4: view image

Paralogs for PTCHD4 Gene

Paralogs for PTCHD4 Gene

(2) SIMAP similar genes for PTCHD4 Gene using alignment to 3 proteins:

  • PTHD4_HUMAN
  • B0QZ29_HUMAN
  • H0Y3Q6_HUMAN

Pseudogenes.org Pseudogenes for PTCHD4 Gene

genes like me logo Genes that share paralogs with PTCHD4: view

Variants for PTCHD4 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PTCHD4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PTCHD4 Gene

Variant ID Type Subtype PubMed ID
esv21548 CNV loss 19812545
esv22426 CNV loss 19812545
esv2671865 CNV deletion 23128226
esv2672027 CNV deletion 23128226
esv3608907 CNV loss 21293372
esv3608909 CNV loss 21293372
nsv1017113 CNV gain 25217958
nsv474998 CNV novel sequence insertion 20440878
nsv603035 CNV loss 21841781
nsv830656 CNV gain 17160897

Variation tolerance for PTCHD4 Gene

Residual Variation Intolerance Score: 1.67% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.13; 38.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTCHD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTCHD4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTCHD4 Gene

Disorders for PTCHD4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PTCHD4 Gene - From: COP

Disorder Aliases PubMed IDs
otopalatodigital syndrome, type i
  • opd1
basal cell nevus syndrome
  • bcns
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PTCHD4

genes like me logo Genes that share disorders with PTCHD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTCHD4 Gene

Publications for PTCHD4 Gene

  1. A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. (PMID: 25296753) Chung JH … Bunz F (The Journal of biological chemistry 2014) 2 3 4
  2. Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium. (PMID: 24823311) Guan W … Steffen LM (Circulation. Cardiovascular genetics 2014) 3
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3

Products for PTCHD4 Gene

Sources for PTCHD4 Gene