ZNF596

protein-coding

zinc finger protein 596, 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. 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_001042416.3

Inheritance

—

ClinVar variants

U:105B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr8:232,137-264,703

External References & Databases

Ensembl (ENSG00000172748)

Transcript & Mutation Effects

hg38 • Region Span ~32.6 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 ZNF596 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042416.3. 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				3 clinvar		3
missense			105 clinvar	3 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	105	6	0	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042416.3	RefSeq	NP_001035881.1	5	MANE Select
ENST00000398612.3	Ensembl	ENSP00000381613.1	5	MANE Select
NM_001042415.3	RefSeq	NP_001035880.1	5	Standard
NM_001287254.2	RefSeq	NP_001274183.1	5	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: ENST00000398612
Coding exons: 5
Length: 15206
Individuals with no LoFs: 125593
Homozygous LoFs: 0
Heterozygous LoFs: 151
Defined: 125744
p: 0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.55	381	264	1.44	0.0000124	3358
Missense (PolyPhen)		132	92.313	1.4299		1191
Synonymous	-2.05	117	92.0	1.27	0.00000439	903
Loss of Function	-0.216	19	18.0	1.05	0.00000109	215

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00098	0.00098	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.00092	0.00091	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.992
RVIS EVS: 0.31
RVIS percentile EVS: 72.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.803

Gene Damage Prediction

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