ZNF599

protein-coding

zinc finger protein 599, 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_001007248.3

Inheritance

—

ClinVar variants

U:93B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr19:34,758,073-34,773,229

External References & Databases

Ensembl (ENSG00000153896)

Transcript & Mutation Effects

hg38 • Region Span ~15.2 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 ZNF599 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007248.3. 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				1 clinvar		1
missense			92 clinvar	6 clinvar		98
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	93	7	0	100

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_001007248.3	RefSeq	NP_001007249.1	4	MANE Select
ENST00000329285.13	Ensembl	ENSP00000333802.6	4	MANE Select
ENST00000587354.6	Ensembl	ENSP00000468446.1	4	Standard
ENST00000588760.1	Ensembl	ENSP00000465262.1	3	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: ENST00000329285
Coding exons: 4
Length: 15154
Individuals with no LoFs: 120434
Homozygous LoFs: 62
Heterozygous LoFs: 5252
Defined: 125748
p: 0.0214

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.128	319	313	1.02	0.0000160	3900
Missense (PolyPhen)		79	93.414	0.84569		1251
Synonymous	1.53	93	114	0.818	0.00000581	1072
Loss of Function	1.66	14	22.5	0.622	0.00000144	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0045	0.0045	notable
Latino/Admixed American	0.0058	0.0057	notable
Ashkenazi Jewish	0.052	0.052	notable
East Asian	0.0014	0.0014	notable
Finnish	0.035	0.035	notable
European (Non-Finnish)	0.023	0.023	notable
South Asian	0.035	0.035	notable
Other	0.017	0.017	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.877
RVIS EVS: 1.42
RVIS percentile EVS: 94.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.537

Gene Damage Prediction

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