ZNF44

protein-coding

zinc finger protein 44, 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 transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF58
ZNF55

MANE transcript

NM_016264.4

Inheritance

—

ClinVar variants

U:87B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr19:12,224,686-12,294,883

External References & Databases

Ensembl (ENSG00000197857)

Transcript & Mutation Effects

hg38 • Region Span ~70.2 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 ZNF44 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016264.4. 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					2 clinvar	2
missense			84 clinvar	2 clinvar	1 clinvar	87
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	87	2	3	92

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016264.4	RefSeq	NP_057348.3	4	MANE Select
ENST00000355684.6	Ensembl	ENSP00000347910.5	4	MANE Select
NM_001164276.2	RefSeq	NP_001157748.1	5	Standard
NM_001353549.2	RefSeq	NP_001340478.1	3	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: ENST00000356109
Coding exons: 5
Length: 70202
Individuals with no LoFs: 125612
Homozygous LoFs: 1
Heterozygous LoFs: 118
Defined: 125731
p: 0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.561	319	348	0.915	0.0000174	4413
Missense (PolyPhen)		128	147.71	0.86656		1981
Synonymous	0.990	104	118	0.884	0.00000569	1162
Loss of Function	1.05	5	8.25	0.606	4.36e-7	91

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00080	0.00079	rare
South Asian	0.000065	0.000065	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0943

Intolerance Scores

LoFtool: 0.959
RVIS EVS: 0.64
RVIS percentile EVS: 84.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0826

Gene Damage Prediction

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