ZNF501

zinc finger protein 501, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:44729596-44737083

Previous symbols: [ "ZNF52" ]

Links

ENSG00000186446 ∙ NCBI:115560 ∙ ∙ HGNC:23717 ∙ Uniprot:Q96CX3 ∙ 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 ZNF501 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF501 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ZNF501

This is a list of pathogenic ClinVar variants found in the ZNF501 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44734425-A-G		not specified	Uncertain significance (Jun 28, 2022)
3-44734438-T-G		not specified	Uncertain significance (Nov 29, 2023)
3-44734467-A-G		not specified	Uncertain significance (Aug 17, 2022)
3-44734508-G-T		not specified	Uncertain significance (Aug 12, 2022)
3-44734520-G-C		not specified	Uncertain significance (Dec 08, 2023)
3-44734600-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-44734650-C-G		not specified	Uncertain significance (Jun 11, 2024)
3-44734657-A-C		not specified	Uncertain significance (May 20, 2024)
3-44734734-C-T		not specified	Uncertain significance (Dec 01, 2022)
3-44734798-G-C		not specified	Uncertain significance (Jul 26, 2021)
3-44734831-C-G		not specified	Uncertain significance (Sep 13, 2023)
3-44734983-A-G		not specified	Uncertain significance (Aug 02, 2021)
3-44735019-A-G		not specified	Uncertain significance (Feb 16, 2023)
3-44735085-G-A		not specified	Uncertain significance (Dec 26, 2023)
3-44735092-A-G		not specified	Uncertain significance (Jul 09, 2021)
3-44735104-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF501	protein_coding	protein_coding	ENST00000396048	1	7488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.281	0.699	125485	0	34	125519	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.529	161	143	1.12	0.00000673	1805
Missense in Polyphen		89	71.167	1.2506		874
Synonymous	-0.695	52	46.0	1.13	0.00000207	475
Loss of Function	1.95	2	7.94	0.252	4.14e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.501
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.146
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;metal ion binding