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Aliases for PTCHD3 Gene

Aliases for PTCHD3 Gene

  • Patched Domain Containing 3 2 3 5
  • Patched-Related Protein 3 4
  • PTR 3 4
  • Patched Domain-Containing Protein 3 3

External Ids for PTCHD3 Gene

Previous GeneCards Identifiers for PTCHD3 Gene

  • GC10M027728

Summaries for PTCHD3 Gene

GeneCards Summary for PTCHD3 Gene

PTCHD3 (Patched Domain Containing 3) is a Protein Coding gene. Diseases associated with PTCHD3 include Epidural Neoplasm and Amelogenesis Imperfecta, Type Ig. Gene Ontology (GO) annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is PTCHD4.

UniProtKB/Swiss-Prot for PTCHD3 Gene

  • May play a role in sperm development or sperm function.

Additional gene information for PTCHD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTCHD3 Gene

Genomics for PTCHD3 Gene

GeneHancer (GH) Regulatory Elements for PTCHD3 Gene

Promoters and enhancers for PTCHD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I027414 Promoter 0.5 EPDnew 550.8 +0.0 1 0.1 PTCHD3 TRIAP1P1
GH10I027449 Enhancer 0.6 Ensembl ENCODE 13.2 -34.8 -34832 0.4 USF1 USF2 MAX PTCHD3 RAB18
GH10I027463 Enhancer 0.5 Ensembl ENCODE 12.5 -50.5 -50545 2.8 SPI1 PTCHD3 ARMC4P1 RAB18
GH10I027391 Enhancer 0.2 ENCODE 20.3 +22.9 22879 1 PTCHD3 TRIAP1P1
GH10I027624 Enhancer 0.7 Ensembl ENCODE 5.8 -211.4 -211397 1.8 POLR2A ZC3H11A ZNF781 ZNF518A MASTL YME1L1 PTCHD3 ABI1 LOC105376463 GC10M027690
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PTCHD3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for PTCHD3 Gene

Genomic Locations for PTCHD3 Gene
16,182 bases
Minus strand

Genomic View for PTCHD3 Gene

Genes around PTCHD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCHD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCHD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTCHD3 Gene

Proteins for PTCHD3 Gene

  • Protein details for PTCHD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Patched domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • I3L499
    • Q6ZU28

    Protein attributes for PTCHD3 Gene

    767 amino acids
    Molecular mass:
    86872 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC86399.1; Type=Erroneous termination; Positions=768; Note=Translated as stop.; Evidence={ECO:0000305};

neXtProt entry for PTCHD3 Gene

Post-translational modifications for PTCHD3 Gene

  • Glycosylation at Asn275, isoforms=279, and Asn678
  • Modification sites at PhosphoSitePlus

Other Protein References for PTCHD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PTCHD3 Gene

Domains & Families for PTCHD3 Gene

Gene Families for PTCHD3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PTCHD3 Gene


Suggested Antigen Peptide Sequences for PTCHD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the patched family.
  • Belongs to the patched family.
genes like me logo Genes that share domains with PTCHD3: view

Function for PTCHD3 Gene

Molecular function for PTCHD3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in sperm development or sperm function.

Phenotypes From GWAS Catalog for PTCHD3 Gene

Gene Ontology (GO) - Molecular Function for PTCHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with PTCHD3: view

Phenotypes for PTCHD3 Gene

GenomeRNAi human phenotypes for PTCHD3:
genes like me logo Genes that share phenotypes with PTCHD3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PTCHD3 Gene

Localization for PTCHD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCHD3 Gene

Membrane; Multi-pass membrane protein. Note=Localizes to the midpiece of the sperm tail. {ECO:0000269 PubMed:17904097}.

Subcellular locations from

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 PTCHD3 gene
Compartment Confidence
plasma membrane 3
extracellular 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PTCHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0097225 sperm midpiece IEA --
genes like me logo Genes that share ontologies with PTCHD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PTCHD3 Gene

Pathways & Interactions for PTCHD3 Gene

SuperPathways for PTCHD3 Gene

No Data Available

Interacting Proteins for PTCHD3 Gene

Gene Ontology (GO) - Biological Process for PTCHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007286 spermatid development NAS 17904097
genes like me logo Genes that share ontologies with PTCHD3: view

No data available for Pathways by source and SIGNOR curated interactions for PTCHD3 Gene

Drugs & Compounds for PTCHD3 Gene

No Compound Related Data Available

Transcripts for PTCHD3 Gene

mRNA/cDNA for PTCHD3 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PTCHD3 Gene

Patched domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTCHD3 Gene

No ASD Table

Relevant External Links for PTCHD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PTCHD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTCHD3 Gene

mRNA differential expression in normal tissues according to GTEx for PTCHD3 Gene

This gene is overexpressed in Testis (x14.3), Adipose - Visceral (Omentum) (x9.5), Pancreas (x7.9), and Breast - Mammary Tissue (x5.8).

NURSA nuclear receptor signaling pathways regulating expression of PTCHD3 Gene:


SOURCE GeneReport for Unigene cluster for PTCHD3 Gene:


mRNA Expression by UniProt/SwissProt for PTCHD3 Gene:

Tissue specificity: Expressed in germ cells of the testis (at protein level).

Evidence on tissue expression from TISSUES for PTCHD3 Gene

  • Nervous system(4.1)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with PTCHD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCHD3 Gene

Orthologs for PTCHD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTCHD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PTCHD3 33 34
  • 98.87 (n)
(Rattus norvegicus)
Mammalia Ptchd3 33
  • 77 (n)
(Mus musculus)
Mammalia Ptchd3 33 16 34
  • 76.08 (n)
(Bos Taurus)
Mammalia LOC516442 33
  • 76.05 (n)
-- 34
  • 56 (a)
-- 34
  • 49 (a)
(Canis familiaris)
Mammalia PTCHD3 33
  • 74.04 (n)
-- 34
  • 62 (a)
-- 34
  • 58 (a)
(Monodelphis domestica)
Mammalia PTCHD3 34
  • 35 (a)
(Gallus gallus)
Aves PTCHD3 33
  • 58.24 (n)
-- 34
  • 42 (a)
-- 34
  • 32 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 33 (a)
-- 34
  • 28 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ptchd3 33
  • 52.7 (n)
(Danio rerio)
Actinopterygii PTCHD3 (3 of 3) 34
  • 45 (a)
PTCHD3 (1 of 3) 34
  • 33 (a)
PTCHD3 (2 of 3) 34
  • 31 (a)
Dr.13837 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010394 33
  • 45.19 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ptr 33 34
  • 44.19 (n)
(Caenorhabditis elegans)
Secernentea ptr-19 33 34
  • 41.1 (n)
ptr-15 34
  • 19 (a)
ptr-2 34
  • 19 (a)
ptr-10 34
  • 18 (a)
daf-6 34
  • 17 (a)
ptr-1 34
  • 17 (a)
ptr-17 34
  • 16 (a)
ptr-20 34
  • 16 (a)
ptr-6 34
  • 16 (a)
ptr-18 34
  • 15 (a)
ptr-9 34
  • 15 (a)
ptr-12 34
  • 14 (a)
ptr-14 34
  • 14 (a)
ptr-22 34
  • 14 (a)
ptr-4 34
  • 14 (a)
ptr-16 34
  • 13 (a)
ptr-3 34
  • 13 (a)
ptr-8 34
  • 13 (a)
ptr-11 34
  • 12 (a)
ptr-13 34
  • 12 (a)
ptr-21 34
  • 12 (a)
ptr-23 34
  • 12 (a)
ptr-5 34
  • 12 (a)
Species where no ortholog for PTCHD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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 PTCHD3 Gene

Gene Tree for PTCHD3 (if available)
Gene Tree for PTCHD3 (if available)

Paralogs for PTCHD3 Gene

Paralogs for PTCHD3 Gene

genes like me logo Genes that share paralogs with PTCHD3: view

Variants for PTCHD3 Gene

Sequence variations from dbSNP and Humsavar for PTCHD3 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs75297921 benign, not specified 27,413,328(-) CCCCCC/CCCCC/CCCCCCC/CCCCCCCC coding_sequence_variant, frameshift
rs1000008712 -- 27,413,995(-) G/A coding_sequence_variant, missense_variant
rs1000300846 -- 27,406,847(-) G/T intron_variant
rs1000757978 -- 27,412,361(-) G/T intron_variant
rs1001107343 -- 27,401,692(-) A/G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PTCHD3 Gene

Variant ID Type Subtype PubMed ID
dgv1006n54 CNV loss 21841781
dgv1008n54 CNV loss 21841781
dgv1010n54 CNV loss 21841781
dgv1013n54 CNV loss 21841781
dgv1014n54 CNV loss 21841781
dgv199e212 CNV loss 25503493
dgv696n100 CNV loss 25217958
dgv74n27 CNV loss 19166990
dgv75n27 CNV loss 19166990
esv1477447 CNV insertion 17803354
esv2676179 CNV deletion 23128226
esv2750889 CNV loss 17911159
esv2750890 CNV loss 17911159
esv2764124 CNV loss 21179565
esv3546059 CNV deletion 23714750
esv3622708 CNV gain 21293372
esv3622714 CNV loss 21293372
esv3622715 CNV gain 21293372
esv3622721 CNV loss 21293372
esv3622722 CNV gain 21293372
esv3622724 CNV gain 21293372
nsv1045257 CNV gain 25217958
nsv1115957 CNV insertion 24896259
nsv466854 CNV loss 19166990
nsv470928 CNV loss 18288195
nsv517741 CNV loss 19592680
nsv550241 CNV gain 21841781
nsv550271 CNV loss 21841781
nsv550277 CNV loss 21841781
nsv550282 CNV loss 21841781
nsv8614 CNV loss 18304495

Variation tolerance for PTCHD3 Gene

Residual Variation Intolerance Score: 94.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.99; 97.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTCHD3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTCHD3 Gene

Disorders for PTCHD3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PTCHD3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
epidural neoplasm
  • extradural tumor
amelogenesis imperfecta, type ig
  • ai1g
robinow syndrome, autosomal recessive
  • rrs
robinow syndrome
  • acral dysostosis with facial and genital abnormalities
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PTCHD3

genes like me logo Genes that share disorders with PTCHD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTCHD3 Gene

Publications for PTCHD3 Gene

  1. Male germ cell-specific expression of a novel Patched-domain containing gene Ptchd3. (PMID: 17904097) Fan J … Zhu GZ (Biochemical and biophysical research communications 2007) 3 4 58
  2. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. (PMID: 22581228) Manning AK … Langenberg C (Nature genetics 2012) 3 58
  3. Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene. (PMID: 21439084) Ghahramani Seno MM … Scherer SW (BMC medical genetics 2011) 3 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 58
  5. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 4 58

Products for PTCHD3 Gene

Sources for PTCHD3 Gene

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