ZNF471

protein-coding

zinc finger protein 471, 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 nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020813.4

Inheritance

—

ClinVar variants

U:86B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr19:56,507,850-56,530,221

External References & Databases

Ensembl (ENSG00000196263)

Transcript & Mutation Effects

hg38 • Region Span ~22.4 kb

Loading mutation effect viewer...

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 ZNF471 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020813.4. 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				1 clinvar		1
missense			86 clinvar	6 clinvar		92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	7	0	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020813.4	RefSeq	NP_065864.2	4	MANE Select
ENST00000308031.10	Ensembl	ENSP00000309161.4	4	MANE Select
NM_001321768.2	RefSeq	NP_001308697.1	2	Standard
ENST00000591537.5	Ensembl	ENSP00000466224.1	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: ENST00000308031
Coding exons: 4
Length: 22379
Individuals with no LoFs: 125572
Homozygous LoFs: 0
Heterozygous LoFs: 168
Defined: 125740
p: 0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.986	273	323	0.846	0.0000149	4204
Missense (PolyPhen)		152	171.76	0.88495		2178
Synonymous	0.677	98	107	0.917	0.00000507	1045
Loss of Function	2.04	12	22.4	0.535	0.00000101	333

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00054	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00047	0.00044	rare
Finnish	0.00044	0.00042	rare
European (Non-Finnish)	0.0011	0.00099	notable
South Asian	0.00046	0.00046	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.738
RVIS EVS: 1.18
RVIS percentile EVS: 92.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.483

Gene Damage Prediction

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