ZNF506

zinc finger protein 506, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:19761038-19821751

Links

ENSG00000081665 ∙ NCBI:440515 ∙ ∙ HGNC:23780 ∙ Uniprot:Q5JVG8 ∙ 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 ZNF506 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF506 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in ZNF506

This is a list of pathogenic ClinVar variants found in the ZNF506 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19794699-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-19794722-T-C		not specified	Uncertain significance (Dec 20, 2023)
19-19794760-T-C		not specified	Uncertain significance (Apr 18, 2023)
19-19794906-G-T		not specified	Uncertain significance (May 30, 2023)
19-19795056-T-G		not specified	Uncertain significance (Apr 12, 2023)
19-19795099-C-T		not specified	Uncertain significance (Mar 11, 2022)
19-19795115-T-C		not specified	Uncertain significance (Apr 19, 2024)
19-19795123-T-C		not specified	Uncertain significance (Nov 20, 2024)
19-19795147-T-C		not specified	Uncertain significance (Jun 18, 2024)
19-19795187-A-G		not specified	Uncertain significance (May 24, 2023)
19-19795288-C-A		not specified	Uncertain significance (Jan 19, 2024)
19-19795322-T-C		not specified	Uncertain significance (Jun 16, 2023)
19-19795325-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-19795328-T-C		not specified	Uncertain significance (Jun 24, 2022)
19-19795366-T-G		not specified	Uncertain significance (Sep 22, 2022)
19-19795373-A-G		not specified	Likely benign (Jul 13, 2021)
19-19795511-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-19795533-T-A		not specified	Uncertain significance (Nov 04, 2023)
19-19795537-C-T		not specified	Uncertain significance (Feb 03, 2022)
19-19795591-A-G		not specified	Uncertain significance (Mar 03, 2022)
19-19795642-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-19795657-A-G		not specified	Uncertain significance (Dec 13, 2022)
19-19806084-T-C		not specified	Uncertain significance (Dec 10, 2024)
19-19806949-G-C		not specified	Uncertain significance (Aug 02, 2023)
19-19806970-T-A		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF506	protein_coding	protein_coding	ENST00000443905	4	35913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-9	0.0647	125446	0	292	125738	0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.909	189	228	0.830	0.0000107	2928
Missense in Polyphen		64	71.62	0.8936		929
Synonymous	-0.272	81	77.9	1.04	0.00000367	768
Loss of Function	-0.231	13	12.1	1.07	5.02e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00477	0.00474
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000277	0.000272
Finnish	0.00126	0.00125
European (Non-Finnish)	0.00106	0.00102
Middle Eastern	0.000277	0.000272
South Asian	0.000296	0.000294
Other	0.00135	0.00130

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: 0.764
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.0623
• hipred: N
• hipred_score: 0.112
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

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