ZNF629

protein-coding

zinc finger protein 629, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF65

MANE transcript

NM_001080417.3

Inheritance

—

ClinVar variants

U:97B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr16:30,778,456-30,787,205

External References & Databases

Ensembl (ENSG00000102870)

Transcript & Mutation Effects

hg38 • Region Span ~8.7 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 ZNF629 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080417.3. 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			96 clinvar	4 clinvar	2 clinvar	102
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	97	5	2	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080417.3	RefSeq	NP_001073886.1	2	MANE Select
ENST00000262525.6	Ensembl	ENSP00000262525.4	2	MANE Select
NM_001345970.2	RefSeq	NP_001332899.1	2	Standard
ENST00000896341.1	Ensembl	ENSP00000566400.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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: ENST00000262525
Coding exons: 2
Length: 8746
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125646
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.86	296	551	0.537	0.0000378	5653
Missense (PolyPhen)		100	317.61	0.31485		3087
Synonymous	2.47	211	262	0.806	0.0000209	1695
Loss of Function	4.78	1	28.5	0.0350	0.00000141	306

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000097	0.0000088	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.161
RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0423

Gene Damage Prediction

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