ZNF554

protein-coding

zinc finger protein 554, 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. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001102651.2

Inheritance

—

ClinVar variants

U:80B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr19:2,819,868-2,836,735

External References & Databases

Ensembl (ENSG00000172006)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 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 ZNF554 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001102651.2. 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				1 clinvar		1
missense			78 clinvar	3 clinvar		81
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	80	4	0	84

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001102651.2	RefSeq	NP_001096121.1	5	MANE Select
ENST00000317243.10	Ensembl	ENSP00000321132.4	5	MANE Select
ENST00000590116.5	Ensembl	ENSP00000464865.1	3	Standard
ENST00000591265.1	Ensembl	ENSP00000467997.1	5	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
metal ion binding

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317243
Coding exons: 5
Length: 15900
Individuals with no LoFs: 125521
Homozygous LoFs: 0
Heterozygous LoFs: 180
Defined: 125701
p: 0.000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.134	282	288	0.978	0.0000157	3526
Missense (PolyPhen)		85	98.409	0.86374		1122
Synonymous	0.319	113	117	0.963	0.00000733	989
Loss of Function	0.894	17	21.5	0.792	0.00000110	267

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.0019	0.0019	notable
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00064	0.00064	rare
South Asian	0.00049	0.00046	rare
Other	0.00082	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.715
RVIS EVS: 0.18
RVIS percentile EVS: 66.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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