PYDC1

protein-coding

pyrin domain containing 1, the group of Pyrin domain containing

Gene summary

Enables protein serine/threonine kinase binding activity and protein serine/threonine kinase inhibitor activity. Involved in innate immune response; negative regulation of signal transduction; and positive regulation of interleukin-1 beta production. Located in cytosol and nucleus. Part of IkappaB kinase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152901.4

Inheritance

—

ClinVar variants

U:13B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr16:31,215,962-31,217,135

External References & Databases

Ensembl (ENSG00000169900)

Transcript & Mutation Effects

hg38 • Region Span ~1.2 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 PYDC1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152901.4. 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			13 clinvar	1 clinvar		14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	1	0	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152901.4	RefSeq	NP_690865.1	1	MANE Select
ENST00000302964.4	Ensembl	ENSP00000304336.4	1	MANE Select
ENST00000928116.1	Ensembl	ENSP00000598175.1	1	Standard
ENST00001136793.1	Ensembl	ENSP00000805694.1	1	Standard

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

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

Molecular Function

cysteine-type endopeptidase activity
protein binding

Cellular Component

nucleus
cytosol
IkappaB kinase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302964
Coding exons: 1
Length: 1398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.130	58	55.3	1.05	0.00000252	557
Missense (PolyPhen)		20	19.376	1.0322		221
Synonymous	0.904	22	28.1	0.783	0.00000129	198
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: 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}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.659
RVIS EVS: 0.24
RVIS percentile EVS: 68.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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