PYGO2

pygopus family PHD finger 2, the group of Wnt enhanceosome complex|PHD finger proteins

Basic information

Region (hg38): 1:154957026-154963853

Links

ENSG00000163348 ∙ NCBI:90780 ∙ OMIM:606903 ∙ HGNC:30257 ∙ Uniprot:Q9BRQ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PYGO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYGO2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in PYGO2

This is a list of pathogenic ClinVar variants found in the PYGO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-154958787-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-154958832-A-G		not specified	Uncertain significance (Mar 20, 2023)
1-154958846-G-A		not specified	Uncertain significance (Mar 29, 2024)
1-154958934-G-A		not specified	Uncertain significance (Sep 26, 2024)
1-154958999-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-154959000-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-154959093-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-154959172-G-C		not specified	Uncertain significance (Apr 22, 2022)
1-154959174-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-154959210-T-G		not specified	Uncertain significance (Oct 03, 2024)
1-154959221-C-A		not specified	Uncertain significance (Mar 03, 2025)
1-154959260-G-A		not specified	Uncertain significance (Apr 22, 2024)
1-154959296-G-A		not specified	Uncertain significance (Aug 19, 2024)
1-154959297-G-A		not specified	Uncertain significance (Feb 12, 2025)
1-154959306-G-C		not specified	Uncertain significance (Jul 30, 2024)
1-154959309-C-G		not specified	Uncertain significance (Mar 31, 2024)
1-154959311-G-A		not specified	Uncertain significance (Feb 22, 2025)
1-154959315-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-154959324-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-154959342-C-A		not specified	Uncertain significance (Sep 25, 2023)
1-154959375-G-C		not specified	Uncertain significance (Feb 14, 2024)
1-154959421-C-A		not specified	Uncertain significance (Aug 12, 2021)
1-154959456-T-G		not specified	Uncertain significance (Feb 28, 2023)
1-154959492-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-154959497-T-C		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYGO2	protein_coding	protein_coding	ENST00000368457	3	6828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0332	125657	0	2	125659	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	161	205	0.784	0.0000109	2584
Missense in Polyphen		39	62.139	0.62762		707
Synonymous	-0.865	91	81.1	1.12	0.00000457	886
Loss of Function	3.01	0	10.6	0.00	6.41e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in signal transduction through the Wnt pathway.
• Pathway: Signaling by WNT;Signal Transduction;Wnt Canonical;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.176
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.739
• ghis: 0.685

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.949

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pygo2
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: in utero embryonic development;kidney development;lens development in camera-type eye;spermatid nucleus differentiation;brain development;post-embryonic development;mammary gland development;regulation of mammary gland epithelial cell proliferation;regulation of histone acetylation;positive regulation of chromatin binding;developmental growth;regulation of histone H3-K4 methylation;roof of mouth development;canonical Wnt signaling pathway;beta-catenin-TCF complex assembly
• Cellular component: nucleoplasm;beta-catenin-TCF complex
• Molecular function: chromatin binding;protein binding;histone acetyltransferase regulator activity;histone binding;metal ion binding