ZNF490

zinc finger protein 490, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12576100-12640098

Links

ENSG00000188033 ∙ NCBI:57474 ∙ OMIM:620118 ∙ HGNC:23705 ∙ Uniprot:Q9ULM2 ∙ 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 ZNF490 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF490 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	1

Variants in ZNF490

This is a list of pathogenic ClinVar variants found in the ZNF490 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12580513-T-G		not specified	Uncertain significance (May 16, 2024)
19-12580520-C-A		not specified	Uncertain significance (Mar 19, 2024)
19-12580520-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-12580715-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-12580799-C-T		not specified	Uncertain significance (Oct 06, 2024)
19-12580910-G-A		not specified	Uncertain significance (May 13, 2024)
19-12581006-T-A		not specified	Uncertain significance (May 31, 2023)
19-12581018-C-T		not specified	Uncertain significance (Jan 27, 2022)
19-12581027-G-C		not specified	Uncertain significance (Sep 16, 2021)
19-12581065-C-T		not specified	Likely benign (Oct 29, 2024)
19-12581073-A-T		not specified	Uncertain significance (Apr 08, 2024)
19-12581077-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-12581107-C-T		not specified	Uncertain significance (Feb 26, 2024)
19-12581110-C-T		not specified	Uncertain significance (May 20, 2024)
19-12581111-G-A		not specified	Uncertain significance (Sep 07, 2022)
19-12581134-G-T		not specified	Uncertain significance (Jun 26, 2023)
19-12581239-T-A		not specified	Uncertain significance (Dec 19, 2023)
19-12581275-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-12581315-C-G		not specified	Uncertain significance (Nov 17, 2022)
19-12581316-C-G		not specified	Uncertain significance (Oct 22, 2021)
19-12581362-C-T		not specified	Uncertain significance (Jun 16, 2024)
19-12581458-C-T		not specified	Uncertain significance (Dec 05, 2024)
19-12581470-G-A		not specified	Uncertain significance (Nov 19, 2022)
19-12581475-C-T			Benign (Feb 05, 2018)
19-12581522-C-T		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF490	protein_coding	protein_coding	ENST00000311437	5	62138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000315	0.599	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	231	291	0.794	0.0000148	3534
Missense in Polyphen		60	96.833	0.61962		1199
Synonymous	-0.150	104	102	1.02	0.00000544	931
Loss of Function	0.603	6	7.82	0.767	3.33e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
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)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.858
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.273
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.870

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;protein binding;metal ion binding