ZFP69B

protein-coding

ZFP69 zinc finger protein B, the group of Zinc fingers C2H2-type|SCAN domain containing

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. Involved in Golgi organization. Located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF643

MANE transcript

NM_023070.3

Inheritance

—

ClinVar variants

U:66B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr1:40,450,102-40,463,718

External References & Databases

Ensembl (ENSG00000187801)

Transcript & Mutation Effects

hg38 • Region Span ~13.6 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 ZFP69B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_023070.3. 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						0
missense			65 clinvar	6 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	66	6	0	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_023070.3	RefSeq	NP_075558.2	5	MANE Select
ENST00000361584.5	Ensembl	ENSP00000354547.4	5	MANE Select
NM_001369565.1	RefSeq	NP_001356494.1	5	Standard
ENST00000411995.6	Ensembl	ENSP00000399664.2	5	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
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000411995
Coding exons: 5
Length: 13617
Individuals with no LoFs: 125593
Homozygous LoFs: 0
Heterozygous LoFs: 154
Defined: 125747
p: 0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.682	241	273	0.884	0.0000129	3528
Missense (PolyPhen)		80	88.459	0.90437		1182
Synonymous	0.231	97	99.9	0.971	0.00000516	954
Loss of Function	0.0278	19	19.1	0.993	8.00e-7	291

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00054	0.00052	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00054	0.00054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00042	0.00041	rare
South Asian	0.0023	0.0021	notable
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 1.11
RVIS percentile EVS: 92.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N

Gene Damage Prediction

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