ZNF28

zinc finger protein 28, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52797408-52857600

Links

ENSG00000198538 ∙ NCBI:7576 ∙ ∙ HGNC:13073 ∙ Uniprot:P17035 ∙ 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 ZNF28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF28 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				1	1	2
missense			60	4	1	65
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	60	7	2

Variants in ZNF28

This is a list of pathogenic ClinVar variants found in the ZNF28 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52799735-A-G		not specified	Uncertain significance (Apr 28, 2022)
19-52799818-G-T		not specified	Uncertain significance (Aug 12, 2024)
19-52799845-T-C		not specified	Uncertain significance (Aug 17, 2022)
19-52799872-C-A		not specified	Uncertain significance (Oct 03, 2022)
19-52799894-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-52799895-G-A			Benign (Jun 19, 2018)
19-52799915-A-C		not specified	Uncertain significance (Jul 20, 2021)
19-52799958-A-T		not specified	Uncertain significance (Jan 15, 2025)
19-52799962-A-C		not specified	Uncertain significance (Sep 13, 2023)
19-52799968-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-52799969-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-52799983-G-A		not specified	Uncertain significance (Dec 06, 2024)
19-52800001-G-A		not specified	Uncertain significance (Dec 07, 2021)
19-52800016-T-A		not specified	Uncertain significance (Jun 06, 2023)
19-52800038-C-T		not specified	Uncertain significance (May 30, 2024)
19-52800056-G-A		not specified	Uncertain significance (Sep 14, 2023)
19-52800080-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-52800112-G-A		not specified	Uncertain significance (Feb 20, 2025)
19-52800174-C-G		not specified	Uncertain significance (Feb 25, 2025)
19-52800196-G-A		not specified	Uncertain significance (May 14, 2024)
19-52800203-C-T		not specified	Uncertain significance (May 20, 2024)
19-52800243-T-A			Likely benign (Oct 01, 2024)
19-52800331-C-T		not specified	Uncertain significance (Mar 04, 2024)
19-52800361-T-C		not specified	Uncertain significance (Jun 06, 2022)
19-52800368-T-G		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF28	protein_coding	protein_coding	ENST00000457749	3	60192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00743	0.558	125617	0	123	125740	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.23	433	367	1.18	0.0000193	4794
Missense in Polyphen		131	139.15	0.94142		1951
Synonymous	-2.05	156	127	1.23	0.00000627	1244
Loss of Function	0.120	3	3.23	0.928	1.38e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000361	0.000358
Ashkenazi Jewish	0.00298	0.00298
East Asian	0.00114	0.00114
Finnish	0.00111	0.00111
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00114	0.00114
South Asian	0.000523	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: 2.05
• rvis_percentile_EVS: 97.76

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Gene ontology

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