ZNF506

protein-coding

zinc finger protein 506, 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. Predicted to be involved in regulation of DNA-templated transcription. Located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001099269.3

Inheritance

—

ClinVar variants

U:57B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr19:19,761,038-19,821,751

External References & Databases

Ensembl (ENSG00000081665)

Transcript & Mutation Effects

hg38 • Region Span ~60.7 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 ZNF506 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099269.3. 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				1 clinvar		1
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	57	3	0	60

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099269.3	RefSeq	NP_001092739.1	4	MANE Select
ENST00000540806.7	Ensembl	ENSP00000440625.1	4	MANE Select
NM_001145404.2	RefSeq	NP_001138876.1	3	Standard
ENST00000443905.6	Ensembl	ENSP00000393835.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000443905
Coding exons: 4
Length: 35913
Individuals with no LoFs: 125446
Homozygous LoFs: 0
Heterozygous LoFs: 292
Defined: 125738
p: 0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.909	189	228	0.830	0.0000107	2928
Missense (PolyPhen)		64	71.62	0.8936		929
Synonymous	-0.272	81	77.9	1.04	0.00000367	768
Loss of Function	-0.231	13	12.1	1.07	5.02e-7	194

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00059	0.00055	rare
Latino/Admixed American	0.0042	0.0034	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00028	0.00027	rare
Finnish	0.0013	0.0012	notable
European (Non-Finnish)	0.0011	0.0010	notable
South Asian	0.00030	0.00029	rare
Other	0.0014	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.764
RVIS EVS: 0.28
RVIS percentile EVS: 71.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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