ZNF217

protein-coding

zinc finger protein 217, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear speck. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006526.3

Inheritance

—

ClinVar variants

U:132B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr20:53,567,071-53,609,907

External References & Databases

Ensembl (ENSG00000171940)

Transcript & Mutation Effects

hg38 • Region Span ~42.8 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 ZNF217 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006526.3. 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			2 clinvar	6 clinvar	7 clinvar	15
missense			129 clinvar	8 clinvar		137
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	132	14	7	153

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006526.3	RefSeq	NP_006517.1	4	MANE Select
ENST00000371471.7	Ensembl	ENSP00000360526.2	4	MANE Select
NM_001385034.1	RefSeq	NP_001371963.1	4	Standard
ENST00000302342.3	Ensembl	ENSP00000304308.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
transcription, DNA-templated
regulation of transcription, DNA-templated
negative regulation of transcription, DNA-templated

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
protein binding

Cellular Component

histone deacetylase complex
nucleoplasm
mitochondrion
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371471
Coding exons: 4
Length: 42843
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.03	523	594	0.881	0.0000357	6930
Missense (PolyPhen)		81	177.32	0.45681		2179
Synonymous	-1.89	287	249	1.15	0.0000187	2027
Loss of Function	5.10	1	32.2	0.0310	0.00000176	438

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the promoters of target genes and functions as repressor. Promotes cell proliferation and antagonizes cell death. Promotes phosphorylation of AKT1 at 'Ser-473'. {ECO:0000269|PubMed:16203743, ECO:0000269|PubMed:16940172, ECO:0000269|PubMed:17259635, ECO:0000269|PubMed:18625718}.;

Recessive Scores

pRec: 0.205

Intolerance Scores

LoFtool: 0.204
RVIS EVS: -0.25
RVIS percentile EVS: 34.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.983

Gene Damage Prediction

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