ZNF544

protein-coding

zinc finger protein 544, 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014480.4

Inheritance

—

ClinVar variants

U:128B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr19:58,228,594-58,277,495

External References & Databases

Ensembl (ENSG00000198131)

Transcript & Mutation Effects

hg38 • Region Span ~48.9 kb

Loading mutation effect viewer...

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 ZNF544 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014480.4. 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			125 clinvar	9 clinvar		134
nonsense						0
start loss						0
frameshift			1 clinvar		1 clinvar	2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	128	11	1	140

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 145 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014480.4	RefSeq	NP_055295.2	4	MANE Select
ENST00000687789.1	Ensembl	ENSP00000510489.1	4	MANE Select
NM_001320767.2	RefSeq	NP_001307696.1	4	Standard
NM_001320769.2	RefSeq	NP_001307698.1	4	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

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269829
Coding exons: 4
Length: 48856
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125736
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.716	412	373	1.10	0.0000185	4726
Missense (PolyPhen)		132	120.22	1.098		1516
Synonymous	-0.396	144	138	1.04	0.00000720	1300
Loss of Function	0.529	5	6.45	0.775	3.63e-7	58

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.938
RVIS EVS: 0.63
RVIS percentile EVS: 83.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.199

Gene Damage Prediction

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