PYDC2

protein-coding

pyrin domain containing 2, the group of Pyrin domain containing

Gene summary

Involved in negative regulation of inflammatory response; negative regulation of interleukin-1 beta production; and negative regulation of signal transduction. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001083308.1

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr3:191,461,163-191,461,456

External References & Databases

Ensembl (ENSG00000253548)

Transcript & Mutation Effects

hg38 • Region Span ~0.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PYDC2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001083308.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	0	0	10

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001083308.1	RefSeq	NP_001076777.1	1	MANE Select
ENST00000518817.1	Ensembl	ENSP00000492367.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

NOD-like receptor signaling pathway - Homo sapiens (human)

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

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000518817
Coding exons: 1
Length: 294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0999	52	50.0	1.04	0.00000230	634
Missense (PolyPhen)		11	14.497	0.75876		223
Synonymous	0.201	20	21.2	0.944	0.00000108	190
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0859

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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