ZNF502

protein-coding

zinc finger protein 502, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in host-mediated activation of viral process and viral release from host cell. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001134442.3

Inheritance

—

ClinVar variants

U:67B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr3:44,712,643-44,723,831

External References & Databases

Ensembl (ENSG00000196653)

Transcript & Mutation Effects

hg38 • Region Span ~11.2 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 ZNF502 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 69

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001134442.3. 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			67 clinvar	3 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	3	0	70

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001134442.3	RefSeq	NP_001127914.1	2	MANE Select
ENST00000436624.7	Ensembl	ENSP00000406469.2	2	MANE Select
NM_001134440.2	RefSeq	NP_001127912.1	2	Standard
NM_001134441.2	RefSeq	NP_001127913.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
positive regulation by host of viral release from host cell
positive regulation by host of viral process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296091
Coding exons: 2
Length: 11189
Individuals with no LoFs: 125671
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125742
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.618	252	281	0.896	0.0000136	3639
Missense (PolyPhen)		76	102.42	0.74204		1313
Synonymous	1.36	76	92.7	0.820	0.00000425	944
Loss of Function	1.11	14	19.2	0.728	0.00000104	285

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00029	0.00029	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Intolerance Scores

LoFtool: 0.670
RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.950

Gene Damage Prediction

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