ZNF493

zinc finger protein 493, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:21397119-21427577

Links

ENSG00000196268 ∙ NCBI:284443 ∙ ∙ HGNC:23708 ∙ Uniprot:Q6ZR52 ∙ 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 ZNF493 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF493 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				1		1
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	3	0

Variants in ZNF493

This is a list of pathogenic ClinVar variants found in the ZNF493 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-21397241-C-A		not specified	Uncertain significance (Apr 23, 2024)
19-21405133-C-A		not specified	Uncertain significance (Jan 16, 2024)
19-21405166-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-21405195-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-21405243-C-G		not specified	Uncertain significance (Jun 17, 2024)
19-21405819-G-C		not specified	Uncertain significance (Dec 21, 2023)
19-21405837-T-G		not specified	Uncertain significance (Jan 07, 2022)
19-21405839-C-T		not specified	Likely benign (Apr 13, 2023)
19-21423022-G-T		not specified	Uncertain significance (May 16, 2024)
19-21423053-T-G		not specified	Uncertain significance (Jul 17, 2023)
19-21423068-G-A		not specified	Uncertain significance (Feb 17, 2022)
19-21423087-A-G		not specified	Uncertain significance (Dec 21, 2022)
19-21423134-T-C		not specified	Uncertain significance (Apr 04, 2023)
19-21423174-A-G		not specified	Uncertain significance (May 16, 2024)
19-21423177-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-21423209-T-G		not specified	Uncertain significance (Jun 18, 2024)
19-21423268-T-A			Likely benign (Sep 01, 2022)
19-21423276-G-C		not specified	Uncertain significance (Dec 02, 2022)
19-21423291-G-A			Likely benign (Aug 01, 2023)
19-21423312-C-A		not specified	Uncertain significance (Jun 02, 2024)
19-21423317-A-G		not specified	Uncertain significance (Jun 02, 2024)
19-21423317-A-T		not specified	Uncertain significance (Oct 25, 2022)
19-21423326-T-A		not specified	Uncertain significance (Mar 20, 2023)
19-21423372-A-G		not specified	Uncertain significance (Nov 06, 2023)
19-21423378-A-G		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF493	protein_coding	protein_coding	ENST00000392288	4	30455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000583	0.150	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.08	450	390	1.15	0.0000179	5108
Missense in Polyphen		147	128.28	1.1459		1792
Synonymous	-0.493	141	134	1.05	0.00000619	1338
Loss of Function	-0.699	7	5.27	1.33	2.23e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000383	0.0000327
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: 0.779
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.2

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.112
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

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