ZNF492

zinc finger protein 492, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:22634324-22667671

Previous symbols: [ "ZNF115" ]

Links

ENSG00000229676 ∙ NCBI:57615 ∙ OMIM:620124 ∙ HGNC:23707 ∙ Uniprot:Q9P255 ∙ 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 ZNF492 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF492 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			52	2		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	0

Variants in ZNF492

This is a list of pathogenic ClinVar variants found in the ZNF492 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-22653419-A-G		not specified	Uncertain significance (Jan 23, 2023)
19-22653967-A-G		not specified	Uncertain significance (Oct 27, 2022)
19-22653983-T-G		not specified	Uncertain significance (Aug 02, 2023)
19-22653999-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-22654000-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-22663850-A-C			Likely benign (Mar 01, 2024)
19-22663856-T-C		not specified	Uncertain significance (Mar 15, 2024)
19-22663872-T-G		not specified	Uncertain significance (Dec 18, 2023)
19-22663883-A-G		not specified	Uncertain significance (Jun 26, 2023)
19-22663959-G-A		not specified	Uncertain significance (May 24, 2023)
19-22663966-T-G		not specified	Uncertain significance (Dec 21, 2023)
19-22664010-A-T		not specified	Uncertain significance (Nov 10, 2022)
19-22664013-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-22664054-A-G		not specified	Likely benign (May 03, 2023)
19-22664064-C-T		not specified	Uncertain significance (Dec 30, 2023)
19-22664090-T-G		not specified	Uncertain significance (Jun 21, 2023)
19-22664126-C-A		not specified	Uncertain significance (Dec 04, 2023)
19-22664151-G-T		not specified	Uncertain significance (Jan 31, 2024)
19-22664159-A-G		not specified	Uncertain significance (Sep 21, 2023)
19-22664356-G-C		not specified	Uncertain significance (Jun 02, 2024)
19-22664411-A-G		not specified	Uncertain significance (May 25, 2022)
19-22664424-C-T		not specified	Uncertain significance (Oct 04, 2022)
19-22664457-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-22664474-A-G		not specified	Uncertain significance (Apr 06, 2024)
19-22664480-C-T		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF492	protein_coding	protein_coding	ENST00000456783	3	33347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.190	0.658	106259	0	5	106264	0.0000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.794	259	225	1.15	0.0000102	3436
Missense in Polyphen		94	86.853	1.0823		1349
Synonymous	-1.33	95	79.9	1.19	0.00000376	895
Loss of Function	0.934	1	2.64	0.379	1.11e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000391	0.0000391
Middle Eastern	0.00	0.00
South Asian	0.0000415	0.0000415
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: 0.702
• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00222

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
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