ZNF790

protein-coding

zinc finger protein 790, 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 active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_206894.4

Inheritance

—

ClinVar variants

U:88

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr19:36,817,428-36,850,787

External References & Databases

Ensembl (ENSG00000197863)

Transcript & Mutation Effects

hg38 • Region Span ~33.4 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 ZNF790 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 83

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_206894.4. 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			2 clinvar			2
missense			86 clinvar			86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	88	0	0	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_206894.4	RefSeq	NP_996777.2	4	MANE Select
ENST00000356725.9	Ensembl	ENSP00000349161.3	4	MANE Select
NM_001242800.2	RefSeq	NP_001229729.1	4	Standard
NM_001242801.2	RefSeq	NP_001229730.1	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

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: ENST00000356725
Coding exons: 4
Length: 33360
Individuals with no LoFs: 123634
Homozygous LoFs: 75
Heterozygous LoFs: 2036
Defined: 125745
p: 0.00843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.168	343	334	1.03	0.0000163	4262
Missense (PolyPhen)		88	86.53	1.017		1146
Synonymous	1.41	92	111	0.830	0.00000535	1075
Loss of Function	0.269	24	25.5	0.943	0.00000151	321

Population LoF Frequency

Population	CAF	p-value	Status
African	0.098	0.098	notable
Latino/Admixed American	0.0067	0.0065	notable
Ashkenazi Jewish	0.012	0.012	notable
East Asian	0.00033	0.00033	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.0015	0.0015	notable
South Asian	0.0017	0.0017	notable
Other	0.0048	0.0047	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.853
RVIS EVS: 0.58
RVIS percentile EVS: 82.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.190

Gene Damage Prediction

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