ZNF71

protein-coding

zinc finger protein 71, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription activator 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_001370215.1

Inheritance

—

ClinVar variants

U:76B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr19:56,595,265-56,626,481

External References & Databases

Ensembl (ENSG00000197951)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 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 ZNF71 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370215.1. 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		2
missense			75 clinvar	1 clinvar	1 clinvar	77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	2	1	79

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370215.1	RefSeq	NP_001357144.1	3	MANE Select
ENST00000599599.7	Ensembl	ENSP00000471138.2	3	MANE Select
NM_001370214.1	RefSeq	NP_001357143.1	1	Standard
NM_021216.5	RefSeq	NP_067039.1	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

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

Molecular Function

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

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328070
Coding exons: 1
Length: 31218
Individuals with no LoFs: 125552
Homozygous LoFs: 0
Heterozygous LoFs: 195
Defined: 125747
p: 0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.693	308	344	0.895	0.0000251	3204
Missense (PolyPhen)		131	179.3	0.73061		1560
Synonymous	0.673	154	165	0.933	0.0000142	936
Loss of Function	0.865	14	18.0	0.780	9.42e-7	176

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00070	0.00069	rare
Ashkenazi Jewish	0.0026	0.0026	notable
East Asian	0.00060	0.00060	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00087	0.00086	rare
South Asian	0.00079	0.00075	rare
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.724
RVIS EVS: 0.13
RVIS percentile EVS: 63.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.728

Gene Damage Prediction

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