ZNF782

protein-coding

zinc finger protein 782, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001001662.3

Inheritance

—

ClinVar variants

U:89B:5

Top phenotype

Mycotic Aneurysm, Intracranial

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr9:96,816,269-96,875,623

External References & Databases

Ensembl (ENSG00000196597)

Transcript & Mutation Effects

hg38 • Region Span ~59.4 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 ZNF782 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 2

Mycotic Aneurysm, IntracranialTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001662.3. 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			88 clinvar	4 clinvar		92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	5	0	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001662.3	RefSeq	NP_001001662.1	4	MANE Select
ENST00000481138.6	Ensembl	ENSP00000419397.1	4	MANE Select
NM_001346991.2	RefSeq	NP_001333920.1	4	Standard
NM_001346993.2	RefSeq	NP_001333922.1	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
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000481138
Coding exons: 4
Length: 59152
Individuals with no LoFs: 125541
Homozygous LoFs: 0
Heterozygous LoFs: 206
Defined: 125747
p: 0.000819

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.254	341	354	0.962	0.0000169	4673
Missense (PolyPhen)		99	103.83	0.95344		1360
Synonymous	0.488	120	127	0.945	0.00000622	1212
Loss of Function	1.26	18	24.7	0.728	0.00000129	374

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.0013	0.0012	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00076	0.00076	rare
South Asian	0.00082	0.00082	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.803
RVIS EVS: 1.18
RVIS percentile EVS: 92.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0940

Gene Damage Prediction

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