ZNF28

protein-coding

zinc finger protein 28, 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, Jul 2025]

MANE transcript

NM_006969.5

Inheritance

—

ClinVar variants

U:127B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr19:52,797,408-52,857,600

External References & Databases

Ensembl (ENSG00000198538)

Transcript & Mutation Effects

hg38 • Region Span ~60.2 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 ZNF28 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 132

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006969.5. 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	1 clinvar	1 clinvar	3
missense			126 clinvar	7 clinvar	1 clinvar	134
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	127	9	2	138

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006969.5	RefSeq	NP_008900.3	3	MANE Select
ENST00000457749.7	Ensembl	ENSP00000397693.2	3	MANE Select
NM_001369761.1	RefSeq	NP_001356690.1	4	Standard
NM_001369762.1	RefSeq	NP_001356691.1	1	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: ENST00000457749
Coding exons: 3
Length: 60192
Individuals with no LoFs: 125617
Homozygous LoFs: 0
Heterozygous LoFs: 123
Defined: 125740
p: 0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.23	433	367	1.18	0.0000193	4794
Missense (PolyPhen)		131	139.15	0.94142		1951
Synonymous	-2.05	156	127	1.23	0.00000627	1244
Loss of Function	0.120	3	3.23	0.928	1.38e-7	35

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.0030	0.0030	notable
East Asian	0.0011	0.0011	notable
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.00052	0.00052	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 2.05
RVIS percentile EVS: 97.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.662

Gene Damage Prediction

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