ZNF280A

protein-coding

zinc finger protein 280A, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a zinc finger protein. The encoded protein contains 4 C2H2-type zinc fingers, which are commonly found in transcription factors. A variety of functions may be performed by this type of zinc finger protein, including the binding of DNA or RNA. [provided by RefSeq, Apr 2014]

Previous symbols:

ZNF280
SUHW1

MANE transcript

NM_080740.5

Inheritance

—

ClinVar variants

U:77B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr22:22,513,736-22,520,270

External References & Databases

Ensembl (ENSG00000169548)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 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 ZNF280A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080740.5. 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				3 clinvar		3
missense			77 clinvar	8 clinvar		85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	11	0	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080740.5	RefSeq	NP_542778.2	1	MANE Select
ENST00000302097.3	Ensembl	ENSP00000302855.3	1	MANE Select
ENST00001131725.1	Ensembl	ENSP00000805605.1	1	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
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: ENST00000302097
Coding exons: 1
Length: 6554
Individuals with no LoFs: 125603
Homozygous LoFs: 0
Heterozygous LoFs: 118
Defined: 125721
p: 0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.563	314	287	1.09	0.0000149	3581
Missense (PolyPhen)		71	65.979	1.0761		990
Synonymous	0.0861	107	108	0.989	0.00000610	1029
Loss of Function	-0.179	11	10.4	1.06	6.19e-7	128

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.0039	0.0039	notable
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00066	0.00065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0771

Intolerance Scores

LoFtool: 0.936
RVIS EVS: 1.38
RVIS percentile EVS: 94.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.999

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High