ZNF608

protein-coding

zinc finger protein 608, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020747.3

Inheritance

—

ClinVar variants

U:179B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr5:124,636,913-124,748,807

External References & Databases

Ensembl (ENSG00000168916)

Transcript & Mutation Effects

hg38 • Region Span ~111.9 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 ZNF608 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020747.3. 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	1 clinvar		4
missense			175 clinvar	2 clinvar		177
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	179	3	0	182

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020747.3	RefSeq	NP_065798.2	9	MANE Select
ENST00000513986.2	Ensembl	ENSP00000421899.2	9	MANE Select
NM_001385619.1	RefSeq	NP_001372548.1	9	Standard
NM_001385620.1	RefSeq	NP_001372549.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II

Molecular Function

nucleic acid binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306315
Coding exons: 9
Length: 111893
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	750	836	0.897	0.0000448	9937
Missense (PolyPhen)		325	413.38	0.78621		4834
Synonymous	-0.686	355	339	1.05	0.0000202	3018
Loss of Function	5.95	3	47.0	0.0639	0.00000226	660

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor, which represses ZNF609 transcription. {ECO:0000250|UniProtKB:Q56A10}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.00599
RVIS EVS: -2.16
RVIS percentile EVS: 1.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.152

Gene Damage Prediction

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