ZFP2

protein-coding

ZFP2 zinc finger protein, 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. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_030613.4

Inheritance

—

ClinVar variants

U:76B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr5:178,895,898-178,933,212

External References & Databases

Ensembl (ENSG00000198939)

Transcript & Mutation Effects

hg38 • Region Span ~37.3 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 ZFP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030613.4. 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			76 clinvar	2 clinvar		78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	2	0	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030613.4	RefSeq	NP_085116.2	1	MANE Select
ENST00000361362.7	Ensembl	ENSP00000354453.2	1	MANE Select
ENST00000520301.5	Ensembl	ENSP00000430980.1	1	Standard
ENST00000520301.6	Ensembl	ENSP00000430980.1	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

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361362
Coding exons: 1
Length: 37319
Individuals with no LoFs: 125485
Homozygous LoFs: 0
Heterozygous LoFs: 259
Defined: 125744
p: 0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0323	243	244	0.994	0.0000116	3080
Missense (PolyPhen)		113	120.88	0.93479		1498
Synonymous	0.497	76	81.7	0.930	0.00000390	805
Loss of Function	-0.994	23	18.4	1.25	0.00000116	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.0044	0.0044	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0014	0.0014	notable
Finnish	0.00055	0.00055	rare
European (Non-Finnish)	0.00042	0.00040	rare
South Asian	0.00043	0.00042	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable transcription factor involved in neuronal differentiation and/or phenotypic maintenance. {ECO:0000250}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.919
RVIS EVS: 0.18
RVIS percentile EVS: 66.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.763

Gene Damage Prediction

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