ZNF662

protein-coding

zinc finger protein 662, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_207404.4

Inheritance

—

ClinVar variants

U:67B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr3:42,906,142-42,919,334

External References & Databases

Ensembl (ENSG00000182983)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 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 ZNF662 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207404.4. 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			66 clinvar	5 clinvar		71
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	6	0	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207404.4	RefSeq	NP_997287.2	4	MANE Select
ENST00000440367.7	Ensembl	ENSP00000405047.2	4	MANE Select
NM_001134656.2	RefSeq	NP_001128128.1	4	Standard
ENST00000328199.6	Ensembl	ENSP00000329264.6	4	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: ENST00000328199
Coding exons: 4
Length: 13603
Individuals with no LoFs: 125257
Homozygous LoFs: 2
Heterozygous LoFs: 489
Defined: 125748
p: 0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.252	260	249	1.04	0.0000130	2985
Missense (PolyPhen)		52	61.249	0.84899		795
Synonymous	0.665	85	93.2	0.912	0.00000515	838
Loss of Function	0.127	19	19.6	0.969	0.00000118	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.0019	0.0019	notable
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.0024	0.0018	notable
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.0023	0.0023	notable
South Asian	0.0020	0.0020	notable
Other	0.0028	0.0028	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.949
RVIS EVS: 0.53
RVIS percentile EVS: 80.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.133

Gene Damage Prediction

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