ZNF486

protein-coding

zinc finger protein 486, 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 extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KRBO2

MANE transcript

NM_052852.4

Inheritance

—

ClinVar variants

U:112B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 1.28

Max pathogenic AF

—

Genomic locus

chr19:20,167,214-20,200,488

External References & Databases

Ensembl (ENSG00000256229)

Transcript & Mutation Effects

hg38 • Region Span ~33.3 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 ZNF486 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 113

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

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052852.4. 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			111 clinvar	3 clinvar		114
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	112	4	0	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052852.4	RefSeq	NP_443084.2	4	MANE Select
ENST00000335117.9	Ensembl	ENSP00000335042.7	4	MANE Select
ENST00000597083.5	Ensembl	ENSP00000469306.1	4	Standard
ENST00000597083.6	Ensembl	ENSP00000469306.1	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, DNA-templated
biological_process

Molecular Function

molecular_function
DNA binding
metal ion binding

Cellular Component

nucleus
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335117
Coding exons: 4
Length: 33263
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125670
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.58	349	237	1.47	0.0000110	3058
Missense (PolyPhen)		131	87.598	1.4955		1151
Synonymous	-3.64	126	83.6	1.51	0.00000418	796
Loss of Function	-0.613	7	5.45	1.28	2.31e-7	66

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.00036	0.00036	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.778
RVIS EVS: 0.38
RVIS percentile EVS: 75.58

Essentials

Essential (CRISPR): N
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