ZNF20

zinc finger protein 20, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12092843-12140355

Links

ENSG00000132010 ∙ NCBI:7568 ∙ OMIM:194557 ∙ HGNC:12992 ∙ Uniprot:P17024 ∙ 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 ZNF20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF20 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						0
missense			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in ZNF20

This is a list of pathogenic ClinVar variants found in the ZNF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12132609-C-A		not specified	Uncertain significance (Jun 21, 2023)
19-12132636-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-12132754-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-12132931-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-12132934-T-C		not specified	Uncertain significance (Apr 12, 2022)
19-12132954-C-T		not specified	Likely benign (Jun 29, 2023)
19-12133023-G-A		not specified	Likely benign (May 27, 2022)
19-12133090-G-A		not specified	Uncertain significance (Nov 01, 2022)
19-12133118-C-A		not specified	Uncertain significance (Dec 19, 2023)
19-12133119-C-T		not specified	Uncertain significance (Nov 06, 2023)
19-12133183-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-12133194-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-12133310-G-C		not specified	Uncertain significance (Nov 14, 2023)
19-12133423-C-T		not specified	Uncertain significance (Sep 14, 2023)
19-12133506-T-C		not specified	Uncertain significance (Sep 07, 2022)
19-12133621-G-A		not specified	Uncertain significance (Apr 10, 2023)
19-12133636-A-C		not specified	Uncertain significance (Sep 20, 2023)
19-12133795-T-C		not specified	Uncertain significance (Jun 22, 2023)
19-12133909-T-A		not specified	Uncertain significance (Jan 23, 2023)
19-12135520-T-A		not specified	Uncertain significance (Dec 22, 2023)
19-12135549-T-G		not specified	Uncertain significance (Oct 20, 2023)
19-12135792-G-T		not specified	Uncertain significance (Oct 03, 2022)
19-12135823-T-G		not specified	Uncertain significance (Nov 09, 2021)
19-12135864-C-T		not specified	Uncertain significance (Oct 27, 2023)
19-12135874-C-T		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF20	protein_coding	protein_coding	ENST00000334213	4	47565

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0966	0.781	125660	1	9	125670	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.647	251	282	0.891	0.0000135	3562
Missense in Polyphen		64	75.681	0.84565		1012
Synonymous	1.37	80	97.2	0.823	0.00000477	920
Loss of Function	1.18	2	4.78	0.418	2.03e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000493	0.000327

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0811

Intolerance Scores

• loftool: 0.716
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.154

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

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;protein binding;metal ion binding