ZNF470

protein-coding

zinc finger protein 470, 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. Located in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001001668.4

Inheritance

—

ClinVar variants

U:126B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.13

Max pathogenic AF

—

Genomic locus

chr19:56,567,468-56,588,911

External References & Databases

Ensembl (ENSG00000197016)

Transcript & Mutation Effects

hg38 • Region Span ~21.4 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 ZNF470 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 131

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001668.4. 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			126 clinvar	6 clinvar		132
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	126	6	0	132

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001668.4	RefSeq	NP_001001668.3	4	MANE Select
ENST00000330619.13	Ensembl	ENSP00000333223.7	4	MANE Select
ENST00000391709.4	Ensembl	ENSP00000375590.3	4	Standard
ENST00000594953.1	Ensembl	ENSP00000472891.1	2	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

Molecular Function

DNA binding
metal ion binding

Cellular Component

nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000330619
Coding exons: 4
Length: 21400
Individuals with no LoFs: 125581
Homozygous LoFs: 1
Heterozygous LoFs: 161
Defined: 125743
p: 0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.979	428	375	1.14	0.0000178	4776
Missense (PolyPhen)		199	172.61	1.1529		2198
Synonymous	0.318	122	127	0.964	0.00000607	1256
Loss of Function	-0.573	27	24.0	1.13	0.00000115	363

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00051	0.00049	rare
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.00066	0.00065	rare
South Asian	0.00093	0.00088	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.655
RVIS EVS: 0.47
RVIS percentile EVS: 78.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0948

Gene Damage Prediction

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