Gene Gene information from NCBI Gene database.
Entrez ID 5309
Gene name Paired like homeodomain 3
Gene symbol PITX3
Synonyms (NCBI Gene)
ASGD1ASMDASODCTPP4CTRCT11PTX3
Chromosome 10
Chromosome location 10q24.32
Summary This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors. This protein is involved in lens formation during eye development. Mutations of this ge
SNPs SNP information provided by dbSNP.
5
SNP ID Visualize variation Clinical significance Consequence
rs104894175 C>T Pathogenic Missense variant, coding sequence variant
rs1057518058 G>A Likely-pathogenic Stop gained, coding sequence variant
rs1411557416 CAGGGCCCCAGGCCCTG>-,CAGGGCCCCAGGCCCTGCAGGGCCCCAGGCCCTG Uncertain-significance, pathogenic Coding sequence variant, frameshift variant
rs1564991147 G>T Likely-pathogenic Stop gained, coding sequence variant
rs1564991256 C>- Pathogenic Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
20
miRTarBase ID miRNA Experiments Reference
MIRT002354 hsa-miR-133b FACSLuciferase reporter assay 17761882
MIRT002354 hsa-miR-133b FACSLuciferase reporter assay 17761882
MIRT512885 hsa-miR-3662 PAR-CLIP 23446348
MIRT512884 hsa-miR-4676-5p PAR-CLIP 23446348
MIRT512883 hsa-miR-575 PAR-CLIP 23446348
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
43
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IEA
GO:0000785 Component Chromatin ISA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602669 9006 ENSG00000107859
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O75364
Protein name Pituitary homeobox 3 (Homeobox protein PITX3) (Paired-like homeodomain transcription factor 3)
Protein function Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons during development. In addition to its importance during development, it also has roles in the long-term surviv
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00046 Homeodomain 63 119 Homeodomain Domain
PF03826 OAR 258 275 OAR motif Motif
Tissue specificity TISSUE SPECIFICITY: Highly expressed in developing eye lens.
Sequence
MEFGLLSEAEARSPALSLSDAGTPHPQLPEHGCKGQEHSDSEKASASLPGGSPEDGSLKK
KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR
ERSQQAELCKGSFAAPLGGLVPPYEEVYPGYSYGNWPPKALAPPLAAKTFPFAFNSVNVG
PLASQPVFSPPSSIAASMVPSAAAAPGTVPGPGALQGLGGGPPGLAPAAVSSGAVSCPYA
SAAAAAAAAASSPYVYRDPCNSSLASLRLKAKQHASFSYPAVHGPPPAANLSPCQYAVER
PV
Sequence length 302
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
27
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Anterior segment dysgenesis 1 Pathogenic; Likely pathogenic rs1411557416 RCV005869604
RCV004787888
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ANTERIOR SEGMENT DYSGENESIS 1, MULTIPLE SUBTYPES Pathogenic rs1411557416 RCV002294347
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract 11 multiple types Likely pathogenic; Pathogenic rs104894175, rs1411557416 RCV000007351
RCV003333078
RCV004559169
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cataract 11, posterior polar Pathogenic rs1564991256, rs1411557416 RCV000043531
RCV002294346
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANHEDONIA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANTERIOR SEGMENT DYSGENESIS 1, MULTIPLE SUBTYPE S Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANTERIOR SEGMENT MESENCHYMAL DYSGENESIS CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Abnormal involuntary movement Abnormal Involuntary Movement BEFREE 30030752
★☆☆☆☆
Found in Text Mining only
Akinesia Akinesia BEFREE 12702666
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis BEFREE 22632920
★☆☆☆☆
Found in Text Mining only
Anhedonia Anhedonia PSYGENET_DG 24480473
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANTERIOR SEGMENT DYSGENESIS 1 Segment dysgenesis GENOMICS_ENGLAND_DG 15286169, 20033184
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ANTERIOR SEGMENT DYSGENESIS 1 Segment dysgenesis CLINVAR_DG 17888164, 24555714
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Anterior segment mesenchymal dysgenesis Anterior segment dysgenesis BEFREE 15665340, 16565358, 18989383, 22223473, 9620774
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anterior segment mesenchymal dysgenesis Anterior segment mesenchymal dysgenesis Pubtator 15665340, 18989383, 20376326, 21836522, 24555714, 36153513 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anterior segment mesenchymal dysgenesis Anterior segment dysgenesis CTD_human_DG 18989383, 9620774
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anterior segment mesenchymal dysgenesis Anterior segment dysgenesis GENOMICS_ENGLAND_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations