MZF1

protein-coding

myeloid zinc finger 1, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

Enables DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein homodimerization activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF42

MANE transcript

NM_198055.2

Inheritance

—

ClinVar variants

U:128B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr19:58,561,931-58,573,575

External References & Databases

Ensembl (ENSG00000099326)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 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 MZF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 130

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198055.2. 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	1 clinvar	1 clinvar	4
missense			124 clinvar	8 clinvar	1 clinvar	133
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	9	2	139

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198055.2	RefSeq	NP_932172.1	5	MANE Select
ENST00000215057.7	Ensembl	ENSP00000215057.1	5	MANE Select
NM_001267033.2	RefSeq	NP_001253962.1	5	Standard
NM_003422.3	RefSeq	NP_003413.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation
overview of telomerase protein component gene htert transcriptional regulation

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215057
Coding exons: 5
Length: 11645
Individuals with no LoFs: 125653
Homozygous LoFs: 0
Heterozygous LoFs: 95
Defined: 125748
p: 0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.262	484	468	1.03	0.0000276	4640
Missense (PolyPhen)		194	204.5	0.94867		2151
Synonymous	-1.95	225	191	1.18	0.0000107	1527
Loss of Function	1.23	19	25.8	0.738	0.00000133	244

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00092	notable
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00074	0.00071	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00033	0.00032	rare
South Asian	0.00034	0.00033	rare
Other	0.00068	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to target promoter DNA and functions as transcription regulator. Regulates transcription from the PADI1 and CDH2 promoter. May be one regulator of transcriptional events during hemopoietic development. {ECO:0000269|PubMed:15541732, ECO:0000269|PubMed:17851584}.;

Recessive Scores

pRec: 0.181

Intolerance Scores

LoFtool: 0.685
RVIS EVS: 1.25
RVIS percentile EVS: 93.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.883

Gene Damage Prediction

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