ZNF280D

protein-coding

zinc finger protein 280D, 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 cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SUHW4

MANE transcript

NM_017661.4

Inheritance

—

ClinVar variants

U:116B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr15:56,630,176-56,734,086

External References & Databases

Ensembl (ENSG00000137871)

Transcript & Mutation Effects

hg38 • Region Span ~103.9 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 ZNF280D variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 109

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017661.4. 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	1 clinvar		3
missense			107 clinvar	4 clinvar		111
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	116	5	0	121

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017661.4	RefSeq	NP_060131.2	20	MANE Select
ENST00000267807.12	Ensembl	ENSP00000267807.7	20	MANE Select
NM_001002843.3	RefSeq	NP_001002843.1	19	Standard
NM_001002844.3	RefSeq	NP_001002844.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

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

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267807
Coding exons: 20
Length: 288391
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125739
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	414	487	0.850	0.0000234	6503
Missense (PolyPhen)		62	111.33	0.55689		1541
Synonymous	-1.33	189	167	1.13	0.00000861	1725
Loss of Function	4.68	12	46.4	0.259	0.00000233	661

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a transcription factor.;

Intolerance Scores

LoFtool: 0.672
RVIS EVS: -0.77
RVIS percentile EVS: 13.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.485

Gene Damage Prediction

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