ZNF816

protein-coding

zinc finger protein 816, 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, Jun 2026]

Previous symbols:

ZNF816A

MANE transcript

NM_001202457.3

Inheritance

—

ClinVar variants

U:93B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.39

Max pathogenic AF

—

Genomic locus

chr19:52,949,379-52,962,911

External References & Databases

Ensembl (ENSG00000180257)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 ZNF816 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001202457.3. 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			93 clinvar	7 clinvar		100
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	11	0	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001202457.3	RefSeq	NP_001189386.1	3	MANE Select
ENST00000444460.7	Ensembl	ENSP00000403266.2	3	MANE Select
NM_001031665.4	RefSeq	NP_001026835.1	3	Standard
NM_001202456.3	RefSeq	NP_001189385.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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: ENST00000357666
Coding exons: 3
Length: 35777
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 56
Defined: 125737
p: 0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0348	338	336	1.01	0.0000171	4335
Missense (PolyPhen)		93	105.24	0.88367		1545
Synonymous	-0.889	124	112	1.11	0.00000529	1128
Loss of Function	-0.684	5	3.60	1.39	1.52e-7	45

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00071	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0016	0.0016	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 2.05
RVIS percentile EVS: 97.76

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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