Aliases for PTCHD3 Gene

Aliases for PTCHD3 Gene

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

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 Autosomal Dominant Non-Syndromic Intellectual Disability 19 and Albinism, Ocular, With Late-Onset Sensorineural Deafness. Gene Ontology (GO) annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is NPC1L1.

UniProtKB/Swiss-Prot Summary for PTCHD3 Gene

Additional gene information for PTCHD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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
GH10J027383 Enhancer 1 Ensembl ENCODE 21.6 +30.3 30346 0.8 TCF12 ZNF639 ZNF10 TCF7 FOXA1 TRIM28 CUX1 TEAD1 TBX3 OSR2 PTCHD3 LRRC37A6P TRIAP1P1
GH10J027502 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 4.6 -90.6 -90612 4.4 EP300 ZBTB40 ZNF217 TCF12 SIN3A NRF1 POLR2G SP1 GTF2E2 JUND RAB18 lnc-MASTL-6 MASTL PTCHD3 piR-52079-025
GH10J027513 Enhancer 1.3 FANTOM5 Ensembl ENCODE 7 -108.4 -108433 19.2 ZBTB40 ATF2 MXI1 ZNF316 FOXA2 ARNT MAFF IRF1 CEBPG MAFK lnc-MASTL-4 RAB18 PTCHD3 MASTL ARMC4P1 FAM210CP ACBD5 piR-52079-025 lnc-MASTL-6 FJ601684-037
GH10J027656 Enhancer 1 Ensembl ENCODE 7.2 -242.4 -242433 0.8 ZNF217 CTCF ZNF639 REST TOE1 RAD21 TRIM22 ATF2 SMC3 MCM3 MASTL YME1L1 WAC-AS1 PTCHD3 piR-43676-004 piR-40110-060
GH10J027391 Enhancer 0.3 ENCODE 20.3 +22.9 22879 1 FOS MYC PTCHD3 TRIAP1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTCHD3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTCHD3

Genomic Locations for PTCHD3 Gene

Genomic Locations for PTCHD3 Gene
17,248 bases
Minus strand
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; Note=Extended C-terminus.; Evidence={ECO:0000305};

neXtProt entry for PTCHD3 Gene

Post-translational modifications for PTCHD3 Gene

  • Glycosylation at Asn275, Asn279, 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

Protein Domains for PTCHD3 Gene


Suggested Antigen Peptide Sequences for PTCHD3 Gene

GenScript: Design optimal peptide antigens:
  • PTCHD3 isoform 2 (F6LPT1_HUMAN)
  • Patched-related protein (PTHD3_HUMAN)

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

No data available for Gene Families for PTCHD3 Gene

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

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCHD3

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 2
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 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

PathCards logo

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

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCHD3

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

No ASD Table

Relevant External Links for PTCHD3 Gene

GeneLoc Exon Structure for

Expression for PTCHD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTCHD3

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 31 30
  • 98.87 (n)
(Rattus norvegicus)
Mammalia Ptchd3 30
  • 77 (n)
(Mus musculus)
Mammalia Ptchd3 17 31 30
  • 76.08 (n)
(Bos Taurus)
Mammalia LOC516442 30
  • 76.05 (n)
-- 31
  • 56 (a)
-- 31
  • 49 (a)
(Canis familiaris)
Mammalia PTCHD3 30
  • 74.04 (n)
-- 31
  • 62 (a)
-- 31
  • 58 (a)
(Monodelphis domestica)
Mammalia PTCHD3 31
  • 35 (a)
(Gallus gallus)
Aves PTCHD3 30
  • 58.24 (n)
-- 31
  • 42 (a)
-- 31
  • 32 (a)
(Anolis carolinensis)
Reptilia -- 31
  • 33 (a)
-- 31
  • 28 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ptchd3 30
  • 52.7 (n)
(Danio rerio)
Actinopterygii PTCHD3 (3 of 3) 31
  • 45 (a)
PTCHD3 (1 of 3) 31
  • 33 (a)
PTCHD3 (2 of 3) 31
  • 31 (a)
Dr.13837 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010394 30
  • 45.19 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ptr 31 30
  • 44.19 (n)
(Caenorhabditis elegans)
Secernentea ptr-19 31 30
  • 41.1 (n)
ptr-2 31
  • 19 (a)
ptr-15 31
  • 19 (a)
ptr-10 31
  • 18 (a)
daf-6 31
  • 17 (a)
ptr-1 31
  • 17 (a)
ptr-6 31
  • 16 (a)
ptr-17 31
  • 16 (a)
ptr-20 31
  • 16 (a)
ptr-9 31
  • 15 (a)
ptr-18 31
  • 15 (a)
ptr-12 31
  • 14 (a)
ptr-22 31
  • 14 (a)
ptr-14 31
  • 14 (a)
ptr-4 31
  • 14 (a)
ptr-8 31
  • 13 (a)
ptr-16 31
  • 13 (a)
ptr-3 31
  • 13 (a)
ptr-23 31
  • 12 (a)
ptr-13 31
  • 12 (a)
ptr-11 31
  • 12 (a)
ptr-5 31
  • 12 (a)
ptr-21 31
  • 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)
Evolutionary constrained regions (ECRs) for PTCHD3: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTCHD3 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs75297921 Benign: not specified 27,413,327(-) G/GC FRAMESHIFT_VARIANT
rs12098477 - p.Thr126Ala
rs12098562 - p.Ala224Gly
rs1638630 - p.Ile584Met
rs2152099 - p.Arg372Lys

Additional dbSNP identifiers (rs#s) for PTCHD3 Gene

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: DISEASES

Disorder Aliases PubMed IDs
autosomal dominant non-syndromic intellectual disability 19
  • autosomal dominant mental retardation 19
albinism, ocular, with late-onset sensorineural deafness
  • albinism, ocular, with sensorineural deafness
epidural neoplasm
  • extradural tumor
retinitis pigmentosa
  • retinitis pigmentosa 1
- 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 54
  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 54
  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 54
  4. 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) 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 54

Products for PTCHD3 Gene

Sources for PTCHD3 Gene