PYDC2

pyrin domain containing 2, the group of Pyrin domain containing

Basic information

Region (hg38): 3:191461163-191461456

Links

ENSG00000253548 ∙ NCBI:152138 ∙ OMIM:615701 ∙ HGNC:33512 ∙ Uniprot:Q56P42 ∙ 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 PYDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYDC2 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in PYDC2

This is a list of pathogenic ClinVar variants found in the PYDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-191461221-A-G		not specified	Uncertain significance (Jan 19, 2022)
3-191461234-C-G		not specified	Uncertain significance (Sep 16, 2021)
3-191461374-C-T		not specified	Uncertain significance (May 28, 2024)
3-191461407-C-T		not specified	Uncertain significance (Dec 07, 2024)
3-191461439-G-A		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYDC2	protein_coding	protein_coding	ENST00000518817	1	294

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	-0.0999	52	50.0	1.04	0.00000230	634
Missense in Polyphen		11	14.497	0.75876		223
Synonymous	0.201	20	21.2	0.944	0.00000108	190
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: May play a role in innate immunity by disrupting the interaction between PYCARD and NLRP3, thereby regulating the NLRP3 inflammasome (PubMed:17339483, PubMed:17178784). May also inhibit NF-kappa-B signaling distally by affecting the nuclear accumulation of RELA (PubMed:17339483, PubMed:24871464). {ECO:0000269|PubMed:17178784, ECO:0000269|PubMed:17339483, ECO:0000269|PubMed:24871464}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0859

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.399

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: inflammatory response;negative regulation of tumor necrosis factor-mediated signaling pathway;negative regulation of NF-kappaB transcription factor activity;innate immune response;negative regulation of interleukin-1 beta secretion;negative regulation of inflammatory response;negative regulation of NLRP3 inflammasome complex assembly;negative regulation of NIK/NF-kappaB signaling
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding