ZNF556

protein-coding

zinc finger protein 556, 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]

MANE transcript

NM_024967.3

Inheritance

—

ClinVar variants

U:76B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr19:2,867,335-2,883,445

External References & Databases

Ensembl (ENSG00000172000)

Transcript & Mutation Effects

hg38 • Region Span ~16.1 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 ZNF556 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024967.3. 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			75 clinvar	11 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	12	0	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024967.3	RefSeq	NP_079243.1	4	MANE Select
ENST00000307635.3	Ensembl	ENSP00000302603.2	4	MANE Select
NM_001300843.2	RefSeq	NP_001287772.1	4	Standard
ENST00000586426.5	Ensembl	ENSP00000467366.1	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
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307635
Coding exons: 4
Length: 11183
Individuals with no LoFs: 124989
Homozygous LoFs: 1
Heterozygous LoFs: 757
Defined: 125747
p: 0.00302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.776	294	259	1.14	0.0000148	2994
Missense (PolyPhen)		89	68.754	1.2945		871
Synonymous	-2.23	132	103	1.28	0.00000697	844
Loss of Function	-0.0193	6	5.95	1.01	2.52e-7	75

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00071	0.00068	rare
Latino/Admixed American	0.00093	0.00078	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00089	0.00088	rare
European (Non-Finnish)	0.0058	0.0055	notable
South Asian	0.0023	0.0019	notable
Other	0.0026	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.697
RVIS EVS: 1.45
RVIS percentile EVS: 95.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.948

Gene Damage Prediction

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