ZNF532

protein-coding

zinc finger protein 532, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in DNA-templated transcription and regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001375912.1

Inheritance

—

ClinVar variants

U:149B:16

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr18:58,862,600-58,986,480

External References & Databases

Ensembl (ENSG00000074657)

Transcript & Mutation Effects

hg38 • Region Span ~123.9 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 ZNF532 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 14

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001375912.1. 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			2 clinvar	5 clinvar	1 clinvar	8
missense			136 clinvar	9 clinvar	1 clinvar	146
nonsense			3 clinvar			3
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	149	14	2	165

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 127 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001375912.1	RefSeq	NP_001362841.1	8	MANE Select
ENST00000591808.6	Ensembl	ENSP00000468238.1	8	MANE Select
NM_001318726.2	RefSeq	NP_001305655.1	8	Standard
NM_001318727.2	RefSeq	NP_001305656.1	8	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: ENST00000336078
Coding exons: 8
Length: 123881
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.68	546	753	0.726	0.0000435	8593
Missense (PolyPhen)		107	239.96	0.44591		3044
Synonymous	-0.745	337	320	1.05	0.0000223	2596
Loss of Function	4.98	6	40.0	0.150	0.00000211	526

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	0.00016	0.00016	rare
Finnish	0.00037	0.00023	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.247
RVIS EVS: -1.39
RVIS percentile EVS: 4.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.128

Gene Damage Prediction

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