ZNF500

zinc finger protein 500, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 16:4748239-4767624

Links

ENSG00000103199 ∙ NCBI:26048 ∙ ∙ HGNC:23716 ∙ Uniprot:O60304 ∙ 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 ZNF500 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF500 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			48	2		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	2	0

Variants in ZNF500

This is a list of pathogenic ClinVar variants found in the ZNF500 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4752389-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-4752402-G-C		not specified	Uncertain significance (Oct 17, 2023)
16-4752419-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-4752439-C-G		not specified	Uncertain significance (Nov 17, 2022)
16-4752446-G-C		not specified	Uncertain significance (Mar 21, 2023)
16-4752467-T-G		not specified	Uncertain significance (Jul 09, 2021)
16-4752471-T-C		not specified	Uncertain significance (Nov 07, 2022)
16-4752473-C-T		not specified	Uncertain significance (May 01, 2023)
16-4752476-C-T		not specified	Uncertain significance (Nov 08, 2022)
16-4752477-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-4752488-C-T		not specified	Uncertain significance (Jul 28, 2021)
16-4752507-T-C		not specified	Uncertain significance (Aug 30, 2022)
16-4752599-C-A		not specified	Uncertain significance (Mar 14, 2023)
16-4752653-C-A		not specified	Uncertain significance (Dec 02, 2022)
16-4752653-C-T		not specified	Uncertain significance (Oct 20, 2023)
16-4752660-C-T		not specified	Uncertain significance (Jan 24, 2024)
16-4752672-A-G		not specified	Uncertain significance (Jan 30, 2024)
16-4752713-C-G		not specified	Uncertain significance (Dec 18, 2023)
16-4752770-T-C		not specified	Uncertain significance (Jan 22, 2024)
16-4752783-T-C		not specified	Uncertain significance (Nov 15, 2023)
16-4752814-G-C		not specified	Uncertain significance (Dec 21, 2022)
16-4752821-C-G		not specified	Uncertain significance (Jan 27, 2022)
16-4752851-T-A		not specified	Uncertain significance (Oct 13, 2023)
16-4752885-G-C		not specified	Uncertain significance (Mar 20, 2023)
16-4752887-G-A		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF500	protein_coding	protein_coding	ENST00000219478	5	19386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000908	0.935	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.67	397	314	1.26	0.0000214	3060
Missense in Polyphen		152	138.47	1.0977		1329
Synonymous	-3.73	195	139	1.40	0.00000993	990
Loss of Function	1.73	11	19.2	0.573	0.00000107	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000164	0.000163
South Asian	0.000265	0.000261
Other	0.000164	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: 0.627
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.12

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.146
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.363

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