ZNF484

zinc finger protein 484, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:92843171-92878038

Links

ENSG00000127081 ∙ NCBI:83744 ∙ ∙ HGNC:23385 ∙ Uniprot:Q5JVG2 ∙ 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 ZNF484 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF484 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			43	2		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	2	0

Variants in ZNF484

This is a list of pathogenic ClinVar variants found in the ZNF484 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-92846251-G-T		not specified	Uncertain significance (Dec 07, 2021)
9-92846299-C-G		not specified	Uncertain significance (Dec 02, 2021)
9-92846368-T-C		not specified	Uncertain significance (Dec 02, 2022)
9-92846379-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-92846382-T-G		not specified	Uncertain significance (Jun 18, 2021)
9-92846455-A-G		not specified	Uncertain significance (May 15, 2024)
9-92846460-T-C		not specified	Uncertain significance (Jan 26, 2022)
9-92846497-G-A		not specified	Uncertain significance (Dec 18, 2023)
9-92846550-T-C		not specified	Uncertain significance (Oct 02, 2023)
9-92846601-A-G		not specified	Uncertain significance (Oct 05, 2023)
9-92846662-T-C		not specified	Uncertain significance (Jul 12, 2022)
9-92846858-C-G		not specified	Uncertain significance (Mar 14, 2023)
9-92847045-A-C		not specified	Uncertain significance (Jan 13, 2023)
9-92847083-A-T		not specified	Uncertain significance (Oct 26, 2022)
9-92847117-C-G		not specified	Uncertain significance (May 27, 2022)
9-92847263-C-G		not specified	Uncertain significance (May 28, 2024)
9-92847408-C-T		not specified	Uncertain significance (Aug 28, 2023)
9-92847453-C-G		not specified	Uncertain significance (Mar 29, 2022)
9-92847478-C-G		not specified	Uncertain significance (May 14, 2024)
9-92847502-T-C		not specified	Uncertain significance (Jun 29, 2023)
9-92847550-C-T		not specified	Uncertain significance (May 17, 2023)
9-92847746-C-G		not specified	Uncertain significance (Oct 05, 2023)
9-92847835-G-C		not specified	Uncertain significance (Mar 02, 2023)
9-92847875-T-C		not specified	Uncertain significance (May 28, 2024)
9-92847916-T-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF484	protein_coding	protein_coding	ENST00000395506	4	32431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-8	0.935	125662	0	82	125744	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	350	439	0.797	0.0000206	5732
Missense in Polyphen		128	180.71	0.70831		2400
Synonymous	1.31	131	152	0.865	0.00000721	1476
Loss of Function	1.90	17	27.8	0.611	0.00000132	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000916	0.000915
Other	0.000328	0.000326

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: 0.0906

Intolerance Scores

• loftool: 0.953
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.148
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.284

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