PYDC1

pyrin domain containing 1, the group of Pyrin domain containing

Basic information

Region (hg38): 16:31215962-31217135

Links

ENSG00000169900 ∙ NCBI:260434 ∙ OMIM:615700 ∙ HGNC:30261 ∙ Uniprot:Q8WXC3 ∙ 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 PYDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYDC1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in PYDC1

This is a list of pathogenic ClinVar variants found in the PYDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-31216782-C-G		not specified	Uncertain significance (Feb 15, 2023)
16-31216796-A-G		not specified	Uncertain significance (Dec 30, 2023)
16-31216806-C-A		not specified	Uncertain significance (Mar 12, 2024)
16-31216838-T-C		not specified	Uncertain significance (Sep 22, 2023)
16-31216841-T-C		not specified	Uncertain significance (Nov 25, 2024)
16-31216868-T-C		not specified	Uncertain significance (May 27, 2022)
16-31216920-C-G		not specified	Likely benign (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYDC1	protein_coding	protein_coding	ENST00000302964	1	1398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	58	55.3	1.05	0.00000252	557
Missense in Polyphen		20	19.376	1.0322		221
Synonymous	0.904	22	28.1	0.783	0.00000129	198
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with PYCARD/ASC and modulates its ability to collaborate with MEFV/pyrin and NLRP3/cryopyrin in NF-kappa-B and pro-caspase-1 activation. Suppresses kinase activity of NF-kappa-B inhibitor kinase (IKK) complex, expression of NF-kappa-B inducible genes and inhibits NF-kappa-B activation by cytokines and LPS. {ECO:0000269|PubMed:12656673, ECO:0000269|PubMed:24871464}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.659
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.0566
• hipred: N
• hipred_score: 0.227
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pop1

Gene ontology

• Biological process: negative regulation of protein kinase activity;proteolysis;negative regulation of tumor necrosis factor-mediated signaling pathway;negative regulation of NF-kappaB transcription factor activity;tumor necrosis factor-mediated signaling pathway;innate immune response;negative regulation of interleukin-1 beta secretion;positive regulation of interleukin-1 beta secretion;negative regulation of NLRP3 inflammasome complex assembly
• Cellular component: nucleus;cytosol;IkappaB kinase complex
• Molecular function: cysteine-type endopeptidase activity;protein binding