ZNF664

protein-coding

zinc finger protein 664, the group of Zinc fingers C2H2-type

Gene summary

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

Previous symbols:

ZNF176

MANE transcript

NM_152437.3

Inheritance

—

ClinVar variants

U:17B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr12:123,971,845-124,015,439

External References & Databases

Ensembl (ENSG00000179195)

Transcript & Mutation Effects

hg38 • Region Span ~43.6 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 ZNF664 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152437.3. 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				1 clinvar		1
missense			17 clinvar			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	1	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152437.3	RefSeq	NP_689650.1	1	MANE Select
ENST00000337815.9	Ensembl	ENSP00000337320.4	1	MANE Select
NM_001204298.2	RefSeq	NP_001191227.1	1	Standard
ENST00000392404.7	Ensembl	ENSP00000376205.3	1	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
biological_process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
molecular_function
DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000539644
Coding exons: 1
Length: 43595
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125736
p: 0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.42	57	137	0.417	0.00000663	1773
Missense (PolyPhen)		17	50.793	0.33469		667
Synonymous	-1.64	63	48.4	1.30	0.00000266	420
Loss of Function	0.688	5	6.96	0.719	2.99e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.0041	0.0041	notable
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.424
RVIS EVS: 0.35
RVIS percentile EVS: 73.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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