ZNF280A

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

Basic information

Region (hg38): 22:22513736-22520270

Previous symbols: [ "ZNF280", "SUHW1" ]

Links

ENSG00000169548 ∙ NCBI:129025 ∙ ∙ HGNC:18597 ∙ Uniprot:P59817 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF280A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF280A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	5	0

Variants in ZNF280A

This is a list of pathogenic ClinVar variants found in the ZNF280A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-22514039-C-G		not specified	Uncertain significance (Feb 25, 2025)
22-22514054-G-A		not specified	Likely benign (Jun 22, 2022)
22-22514060-T-C		not specified	Uncertain significance (Nov 20, 2024)
22-22514075-G-A		not specified	Uncertain significance (Jul 13, 2021)
22-22514078-G-C		not specified	Uncertain significance (Mar 07, 2023)
22-22514087-G-A		not specified	Uncertain significance (Apr 07, 2023)
22-22514091-C-A		not specified	Uncertain significance (Feb 08, 2025)
22-22514118-T-A		not specified	Uncertain significance (Oct 12, 2022)
22-22514129-C-T		not specified	Uncertain significance (Feb 08, 2025)
22-22514139-C-G		not specified	Uncertain significance (Dec 14, 2022)
22-22514192-G-A		not specified	Uncertain significance (Dec 10, 2024)
22-22514246-G-A		not specified	Uncertain significance (Aug 20, 2024)
22-22514255-T-C		not specified	Uncertain significance (Nov 28, 2023)
22-22514261-C-T		not specified	Uncertain significance (Feb 01, 2025)
22-22514316-T-C		not specified	Uncertain significance (Dec 02, 2024)
22-22514336-A-G		not specified	Uncertain significance (May 02, 2024)
22-22514412-C-T		not specified	Uncertain significance (Nov 22, 2023)
22-22514420-G-A		not specified	Uncertain significance (Jan 10, 2023)
22-22514454-G-C		not specified	Uncertain significance (Jul 14, 2021)
22-22514499-C-T		not specified	Uncertain significance (Feb 27, 2023)
22-22514538-C-G		not specified	Uncertain significance (Oct 24, 2023)
22-22514553-T-C		not specified	Uncertain significance (Jan 30, 2024)
22-22514609-C-T		not specified	Uncertain significance (Sep 26, 2024)
22-22514610-G-A		not specified	Uncertain significance (Jan 10, 2022)
22-22514615-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF280A	protein_coding	protein_coding	ENST00000302097	1	6554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.02e-8	0.112	125603	0	118	125721	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.563	314	287	1.09	0.0000149	3581
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000934	0.000934
Ashkenazi Jewish	0.00388	0.00388
East Asian	0.000273	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000273	0.000272
South Asian	0.000656	0.000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0789
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;metal ion binding