ZNF780B

protein-coding

zinc finger protein 780B, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription activator 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]

Previous symbols:

ZNF779

MANE transcript

NM_001005851.3

Inheritance

—

ClinVar variants

U:110B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr19:40,028,260-40,056,231

External References & Databases

Ensembl (ENSG00000128000)

Transcript & Mutation Effects

hg38 • Region Span ~28.0 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 ZNF780B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 114

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001005851.3. 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			108 clinvar	6 clinvar		114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	110	6	0	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001005851.3	RefSeq	NP_001005851.1	4	MANE Select
ENST00000434248.6	Ensembl	ENSP00000391641.1	4	MANE Select
ENST00000221355.10	Ensembl	ENSP00000221355.6	1	Standard
ENST00000593605.1	Ensembl	ENSP00000471501.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000434248
Coding exons: 4
Length: 27950
Individuals with no LoFs: 123680
Homozygous LoFs: 9
Heterozygous LoFs: 2054
Defined: 125743
p: 0.00824

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.408	459	435	1.05	0.0000219	5596
Missense (PolyPhen)		109	100.29	1.0869		1219
Synonymous	-1.09	157	141	1.12	0.00000648	1430
Loss of Function	0.468	4	5.15	0.777	2.17e-7	63

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0022	notable
Latino/Admixed American	0.0034	0.0034	notable
Ashkenazi Jewish	0.0080	0.0080	notable
East Asian	0.00027	0.00027	rare
Finnish	0.0076	0.0076	notable
European (Non-Finnish)	0.013	0.013	notable
South Asian	0.0039	0.0039	notable
Other	0.0075	0.0075	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.705
RVIS EVS: 1.29
RVIS percentile EVS: 93.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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