ZNF696

protein-coding

zinc finger protein 696, 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_030895.3

Inheritance

—

ClinVar variants

U:74B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr8:143,289,676-143,299,952

External References & Databases

Ensembl (ENSG00000185730)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

Loading mutation effect viewer...

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 ZNF696 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030895.3. 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 clinvar		2
missense			72 clinvar	2 clinvar		74
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	3	0	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030895.3	RefSeq	NP_112157.2	2	MANE Select
ENST00000330143.8	Ensembl	ENSP00000328515.3	2	MANE Select
ENST00000518432.5	Ensembl	ENSP00000428856.1	2	Standard
ENST00000518575.5	Ensembl	ENSP00000427857.1	2	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: ENST00000330143
Coding exons: 2
Length: 8386
Individuals with no LoFs: 125334
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125349
p: 0.0000598

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.180	235	243	0.968	0.0000195	2348
Missense (PolyPhen)		71	83.741	0.84785		791
Synonymous	0.300	111	115	0.964	0.0000106	741
Loss of Function	1.73	2	6.90	0.290	3.00e-7	71

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0.00011	0.000092	rare
European (Non-Finnish)	0.000060	0.000053	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.279

Gene Damage Prediction

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