PYGO1

pygopus family PHD finger 1, the group of PHD finger proteins|Wnt enhanceosome complex

Basic information

Region (hg38): 15:55538884-55588947

Links

ENSG00000171016 ∙ NCBI:26108 ∙ OMIM:606902 ∙ HGNC:30256 ∙ Uniprot:Q9Y3Y4 ∙ 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 PYGO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYGO1 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in PYGO1

This is a list of pathogenic ClinVar variants found in the PYGO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-55546029-A-C		not specified	Uncertain significance (Apr 01, 2025)
15-55546051-C-T		not specified	Uncertain significance (Jan 19, 2024)
15-55546054-A-G		not specified	Uncertain significance (May 16, 2025)
15-55546261-T-C		not specified	Uncertain significance (May 25, 2025)
15-55546288-T-A		not specified	Uncertain significance (Sep 30, 2024)
15-55546318-C-G		not specified	Uncertain significance (Jun 25, 2024)
15-55546334-A-G		not specified	Uncertain significance (Apr 12, 2025)
15-55546375-G-A		not specified	Uncertain significance (Mar 03, 2025)
15-55546376-T-A		not specified	Uncertain significance (Nov 14, 2023)
15-55546444-T-C		not specified	Uncertain significance (Dec 27, 2023)
15-55546499-T-C		not specified	Uncertain significance (Apr 02, 2025)
15-55546552-C-T		not specified	Uncertain significance (Sep 11, 2024)
15-55546556-G-C		not specified	Uncertain significance (May 01, 2025)
15-55546574-G-T		not specified	Uncertain significance (Aug 16, 2021)
15-55546636-A-G		not specified	Uncertain significance (Jun 24, 2022)
15-55546681-G-C		not specified	Uncertain significance (Jun 25, 2024)
15-55546688-C-T		not specified	Uncertain significance (Jun 06, 2023)
15-55546690-G-T		not specified	Uncertain significance (Jan 09, 2024)
15-55546723-A-C		not specified	Uncertain significance (Jul 25, 2023)
15-55546730-T-G		not specified	Uncertain significance (Jan 26, 2025)
15-55546742-C-A		not specified	Uncertain significance (Apr 22, 2022)
15-55546754-T-C		not specified	Uncertain significance (Sep 14, 2023)
15-55546778-C-G		not specified	Uncertain significance (Jul 14, 2021)
15-55546814-C-T		not specified	Uncertain significance (Apr 03, 2025)
15-55546874-C-G		not specified	Uncertain significance (May 20, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYGO1	protein_coding	protein_coding	ENST00000302000	3	50058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0132	125722	0	2	125724	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.109	232	227	1.02	0.0000118	2773
Missense in Polyphen		73	77.159	0.9461		906
Synonymous	-0.542	90	83.7	1.08	0.00000462	829
Loss of Function	3.35	0	13.1	0.00	8.02e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000546	0.0000544
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: Wnt-beta-catenin Signaling Pathway in Leukemia;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: 0.117

Intolerance Scores

• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.0892
• hipred: Y
• hipred_score: 0.853
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.440

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pygo1
• Phenotype: cellular phenotype; growth/size/body region 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); vision/eye phenotype; renal/urinary system phenotype; reproductive 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); normal phenotype

Gene ontology

• Biological process: kidney development;hematopoietic progenitor cell differentiation;spermatid nucleus differentiation;post-embryonic development;protein localization to nucleus;positive regulation of transcription by RNA polymerase II;canonical Wnt signaling pathway;beta-catenin-TCF complex assembly
• Cellular component: nucleoplasm
• Molecular function: protein binding;methylated histone binding;metal ion binding