ZNF620

zinc finger protein 620, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:40477131-40518736

Links

ENSG00000177842 ∙ NCBI:253639 ∙ ∙ HGNC:28742 ∙ Uniprot:Q6ZNG0 ∙ 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 ZNF620 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF620 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			44	1		45
Total	0	0	59	1	0

Variants in ZNF620

This is a list of pathogenic ClinVar variants found in the ZNF620 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-40477984-T-C		not specified	Uncertain significance (May 17, 2023)
3-40477998-T-G		not specified	Uncertain significance (Jun 29, 2023)
3-40481867-T-C		not specified	Uncertain significance (Oct 06, 2021)
3-40482001-A-G		not specified	Uncertain significance (Dec 05, 2023)
3-40482236-C-T		not specified	Uncertain significance (Apr 13, 2022)
3-40482245-G-T		not specified	Uncertain significance (Sep 28, 2022)
3-40482276-G-T		not specified	Uncertain significance (Nov 17, 2022)
3-40482301-C-A		not specified	Uncertain significance (Nov 22, 2023)
3-40482334-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-40482343-C-T		not specified	Uncertain significance (Apr 22, 2024)
3-40482617-A-G		not specified	Uncertain significance (Jun 05, 2024)
3-40482641-G-A		not specified	Uncertain significance (Aug 16, 2022)
3-40482674-G-C		not specified	Uncertain significance (Aug 08, 2023)
3-40482677-G-A		not specified	Uncertain significance (Nov 13, 2023)
3-40486818-A-G		not specified	Uncertain significance (Jan 04, 2024)
3-40486838-A-C		not specified	Uncertain significance (Dec 11, 2023)
3-40486952-C-G		not specified	Uncertain significance (Dec 28, 2022)
3-40487009-G-T		not specified	Uncertain significance (Oct 17, 2023)
3-40487028-C-G		not specified	Uncertain significance (Nov 17, 2023)
3-40487042-A-G		not specified	Uncertain significance (Mar 29, 2022)
3-40487099-T-G		not specified	Uncertain significance (Mar 28, 2023)
3-40487175-A-G		not specified	Uncertain significance (Nov 13, 2023)
3-40487175-A-T		not specified	Uncertain significance (May 24, 2024)
3-40487179-G-C		not specified	Uncertain significance (Apr 08, 2022)
3-40487256-G-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF620	protein_coding	protein_coding	ENST00000314529	4	12745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000420	0.867	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.710	192	222	0.866	0.0000104	2802
Missense in Polyphen		55	61.263	0.89776		747
Synonymous	0.377	78	82.4	0.947	0.00000399	761
Loss of Function	1.34	7	12.0	0.583	5.93e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000560	0.000560
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000984	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
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

• loftool: 0.762
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.148
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

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