ZNF546

protein-coding

zinc finger protein 546, 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 transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF49

MANE transcript

NM_178544.5

Inheritance

—

ClinVar variants

U:129B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr19:39,984,134-40,021,038

External References & Databases

Ensembl (ENSG00000187187)

Transcript & Mutation Effects

hg38 • Region Span ~36.9 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 ZNF546 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 130

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178544.5. 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	2 clinvar		3
missense			128 clinvar	4 clinvar		132
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	129	6	0	135

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178544.5	RefSeq	NP_848639.2	5	MANE Select
ENST00000347077.9	Ensembl	ENSP00000339823.3	5	MANE Select
NM_001297763.2	RefSeq	NP_001284692.1	5	Standard
ENST00000595225.1	Ensembl	ENSP00000472403.1	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 by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000347077
Coding exons: 5
Length: 33474
Individuals with no LoFs: 125226
Homozygous LoFs: 0
Heterozygous LoFs: 521
Defined: 125747
p: 0.00207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.282	449	466	0.963	0.0000242	5580
Missense (PolyPhen)		45	52.613	0.8553		495
Synonymous	1.15	133	151	0.881	0.00000776	1467
Loss of Function	1.75	23	34.0	0.676	0.00000203	439

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00093	0.00092	rare
Latino/Admixed American	0.0025	0.0025	notable
Ashkenazi Jewish	0.0091	0.0092	notable
East Asian	0.00084	0.00082	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.0020	0.0020	notable
South Asian	0.0021	0.0021	notable
Other	0.0031	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.883
RVIS EVS: 0.61
RVIS percentile EVS: 82.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0671

Gene Damage Prediction

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