ZFP69

protein-coding

ZFP69 zinc finger protein, the group of SCAN domain containing|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 lipid metabolic process and regulation of transcription by RNA polymerase II. Predicted to be located in nuclear lumen. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF642

MANE transcript

NM_001320179.2

Inheritance

—

ClinVar variants

U:74B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr1:40,477,290-40,496,343

External References & Databases

Ensembl (ENSG00000187815)

Transcript & Mutation Effects

hg38 • Region Span ~19.1 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 ZFP69 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001320179.2. 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			71 clinvar	3 clinvar	1 clinvar	75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	74	4	1	79

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001320179.2	RefSeq	NP_001307108.1	5	MANE Select
ENST00000372706.6	Ensembl	ENSP00000361791.1	5	MANE Select
NM_001320178.2	RefSeq	NP_001307107.1	5	Standard
NM_198494.3	RefSeq	NP_940896.2	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
lipid metabolic process
regulation of lipid metabolic process

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: ENST00000372706
Coding exons: 5
Length: 19129
Individuals with no LoFs: 125501
Homozygous LoFs: 1
Heterozygous LoFs: 246
Defined: 125748
p: 0.000983

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.22	229	287	0.798	0.0000140	3517
Missense (PolyPhen)		75	112.2	0.66843		1396
Synonymous	1.42	84	102	0.821	0.00000544	922
Loss of Function	1.19	15	20.9	0.718	9.59e-7	295

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.0019	0.0018	notable
South Asian	0.00016	0.00016	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative transcription factor that appears to regulate lipid metabolism. {ECO:0000250|UniProtKB:A2A761}.;

Recessive Scores

pRec: 0.0932

Intolerance Scores

RVIS EVS: 0.87
RVIS percentile EVS: 88.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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