ZNF425

protein-coding

zinc finger protein 425, 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 transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of DNA-templated transcription. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001001661.3

Inheritance

—

ClinVar variants

U:107B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr7:149,102,784-149,126,324

External References & Databases

Ensembl (ENSG00000204947)

Transcript & Mutation Effects

hg38 • Region Span ~23.5 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 ZNF425 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 112

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001661.3. 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			107 clinvar	6 clinvar		113
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	107	6	0	113

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001661.3	RefSeq	NP_001001661.1	4	MANE Select
ENST00000378061.7	Ensembl	ENSP00000367300.2	4	MANE Select
ENST00000483014.1	Ensembl	ENSP00000420379.1	4	Standard
ENST00000926832.1	Ensembl	ENSP00000596891.1	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
negative regulation of transcription, DNA-templated

Molecular Function

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

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378061
Coding exons: 4
Length: 23563
Individuals with no LoFs: 125709
Homozygous LoFs: 1
Heterozygous LoFs: 37
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	403	471	0.855	0.0000306	4994
Missense (PolyPhen)		120	127.64	0.94013		1514
Synonymous	-0.483	209	200	1.04	0.0000142	1370
Loss of Function	0.171	7	7.51	0.933	3.21e-7	84

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00082	0.00082	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.00056	0.00052	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional repressor. {ECO:0000269|PubMed:21266108}.;

Intolerance Scores

LoFtool: 0.897
RVIS EVS: -0.33
RVIS percentile EVS: 30.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.479

Gene Damage Prediction

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