ZNF706

protein-coding

zinc finger protein 706

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of stem cell population maintenance. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016096.5

Inheritance

—

ClinVar variants

U:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr8:101,177,878-101,206,193

External References & Databases

Ensembl (ENSG00000120963)

Transcript & Mutation Effects

hg38 • Region Span ~28.3 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 ZNF706 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016096.5. 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						0
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	3	0	0	3

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 82 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016096.5	RefSeq	NP_057180.1	2	MANE Select
ENST00000311212.9	Ensembl	ENSP00000311768.4	2	MANE Select
NM_001042510.2	RefSeq	NP_001035975.1	2	Standard
NM_001267708.2	RefSeq	NP_001254637.1	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 translation
negative regulation of transcription, DNA-templated
negative regulation of stem cell population maintenance

Molecular Function

metal ion binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000520347
Coding exons: 2
Length: 28316
Individuals with no LoFs: 125627
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125628
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	8	38.9	0.206	0.00000181	496
Missense (PolyPhen)
Synonymous	-0.218	13	12.0	1.08	5.15e-7	130
Loss of Function	1.85	0	3.98	0.00	1.68e-7	49

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription repressor involved in the exit of embryonic stem cells (ESCs) from self-renewal. Acts by repressing expression of KLF4. {ECO:0000250|UniProtKB:Q9D115}.;

Recessive Scores

pRec: 0.0341

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 63.81

Essentials

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

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low