ZNF658

protein-coding

zinc finger protein 658, the group of Zinc fingers C2H2-type

Gene summary

Enables transcription cis-regulatory region binding activity. Involved in cellular response to zinc ion; negative regulation of DNA-templated transcription; and ribosome biogenesis. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_033160.7

Inheritance

—

ClinVar variants

U:183B:14

Top phenotype

—

Max pathogenic AF

—

Genomic locus

chr9:66,856,426-66,932,141

External References & Databases

Ensembl (ENSG00000274349)

Transcript & Mutation Effects

hg38 • Region Span ~75.7 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 ZNF658 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 194

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033160.7. 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		2
missense			183 clinvar	12 clinvar		195
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	183	14	0	197

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033160.7	RefSeq	NP_149350.3	4	MANE Select
ENST00000621410.5	Ensembl	ENSP00000482447.1	4	MANE Select
NM_001317916.2	RefSeq	NP_001304845.1	4	Standard
ENST00000612867.4	Ensembl	ENSP00000482540.1	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
ribosome biogenesis
negative regulation of transcription, DNA-templated
cellular response to zinc ion

Molecular Function

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

Cellular Component

nucleus

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates transcriptional repression in response to zinc. Represses several genes, including SLC30A5, SLC30A10 and CBWD1, by binding to the zinc transcriptional regulatory element (ZTRE) (5'- C[AC]C[TAG]CC[TC]-N(0-50)-[GA]G[ATC]G[TG]G-3') found in the promoter region. May play a role in the control of ribosome biogenesis, regulating predominantly rRNA levels, as well as those of several ribosomal proteins, thus coordinating this highly zinc- demanding process with the available zinc supply. {ECO:0000269|PubMed:25582195}.;

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.390

Gene Damage Prediction

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