ZNF621

zinc finger protein 621, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:40524878-40574685

Links

ENSG00000172888 ∙ NCBI:285268 ∙ ∙ HGNC:24787 ∙ Uniprot:Q6ZSS3 ∙ 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 ZNF621 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF621 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			22	3		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in ZNF621

This is a list of pathogenic ClinVar variants found in the ZNF621 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-40529355-A-G		not specified	Uncertain significance (Jan 10, 2025)
3-40529376-C-T		not specified	Uncertain significance (May 15, 2024)
3-40529403-G-A		not specified	Likely benign (Sep 28, 2022)
3-40529403-G-C		not specified	Likely benign (Mar 14, 2025)
3-40530242-C-T		not specified	Uncertain significance (Jan 07, 2025)
3-40530277-G-A		not specified	Uncertain significance (Feb 26, 2025)
3-40532041-T-C		not specified	Uncertain significance (Nov 24, 2024)
3-40532043-G-T		not specified	Uncertain significance (Nov 20, 2024)
3-40532057-G-A		not specified	Likely benign (Jul 09, 2021)
3-40532090-C-T		not specified	Uncertain significance (Jan 23, 2025)
3-40532101-A-G		not specified	Uncertain significance (Jun 25, 2024)
3-40532119-C-T		not specified	Uncertain significance (Nov 28, 2023)
3-40532252-G-A		not specified	Uncertain significance (Jan 19, 2025)
3-40532321-G-A		not specified	Uncertain significance (Jun 07, 2024)
3-40532324-G-A		not specified	Uncertain significance (May 18, 2023)
3-40532383-G-A		not specified	Uncertain significance (Jan 27, 2025)
3-40532450-G-A		not specified	Uncertain significance (Feb 10, 2025)
3-40532474-A-G		not specified	Uncertain significance (Dec 24, 2024)
3-40532503-C-A		not specified	Uncertain significance (Aug 29, 2022)
3-40532503-C-T		not specified	Uncertain significance (Jan 26, 2023)
3-40532509-A-C		not specified	Uncertain significance (Jun 29, 2022)
3-40532566-A-G		not specified	Uncertain significance (Nov 02, 2021)
3-40532652-G-C		not specified	Uncertain significance (Dec 17, 2024)
3-40532711-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-40532750-C-G		not specified	Uncertain significance (Jul 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF621	protein_coding	protein_coding	ENST00000339296	4	49808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000105	0.813	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.478	212	233	0.912	0.0000115	2861
Missense in Polyphen		64	73.343	0.87261		944
Synonymous	0.540	82	88.5	0.927	0.00000472	860
Loss of Function	1.30	10	15.5	0.644	8.11e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000218	0.000217
South Asian	0.000490	0.000490
Other	0.00	0.00

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: 0.665
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.0972
• hipred: N
• hipred_score: 0.148
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.432

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: nuclear speck
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding