ZNF530

zinc finger protein 530, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57599884-57612722

Links

ENSG00000183647 ∙ NCBI:348327 ∙ ∙ HGNC:29297 ∙ Uniprot:Q6P9A1 ∙ 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 ZNF530 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF530 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				3		3
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	5	0

Variants in ZNF530

This is a list of pathogenic ClinVar variants found in the ZNF530 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57604371-T-C		not specified	Uncertain significance (Jan 31, 2022)
19-57604375-G-C		not specified	Uncertain significance (Dec 06, 2023)
19-57604388-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-57605733-G-A		not specified	Likely benign (Oct 25, 2023)
19-57605817-C-T		not specified	Uncertain significance (Apr 22, 2022)
19-57605857-C-A		not specified	Uncertain significance (Apr 22, 2022)
19-57605901-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-57605944-A-G		not specified	Uncertain significance (Mar 07, 2024)
19-57606148-G-A		not specified	Likely benign (May 29, 2024)
19-57606249-A-G		not specified	Uncertain significance (Jun 07, 2024)
19-57606277-G-A		not specified	Uncertain significance (Dec 20, 2021)
19-57606344-G-C			Likely benign (Jan 01, 2024)
19-57606358-G-A		not specified	Uncertain significance (Mar 28, 2023)
19-57606380-C-T			Likely benign (Jan 01, 2024)
19-57606384-A-C			Likely benign (Jan 01, 2024)
19-57606439-G-A		not specified	Uncertain significance (Sep 14, 2021)
19-57606439-G-T		not specified	Uncertain significance (Feb 03, 2023)
19-57606471-G-A		not specified	Uncertain significance (Jun 30, 2022)
19-57606541-A-G		not specified	Uncertain significance (Dec 20, 2022)
19-57606630-C-A		not specified	Uncertain significance (Dec 31, 2023)
19-57606661-A-T		not specified	Uncertain significance (Mar 28, 2023)
19-57606709-T-C		not specified	Uncertain significance (Oct 02, 2023)
19-57606880-G-A		not specified	Likely benign (Mar 15, 2024)
19-57606966-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-57607030-G-A		not specified	Likely benign (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF530	protein_coding	protein_coding	ENST00000332854	3	12838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00744	0.558	125341	0	3	125344	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.114	306	312	0.982	0.0000152	3966
Missense in Polyphen		76	91.998	0.82611		1230
Synonymous	-0.595	121	113	1.07	0.00000558	1112
Loss of Function	0.121	3	3.23	0.928	1.39e-7	34

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)	0.0000276	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.838
• rvis_EVS: 1.82
• rvis_percentile_EVS: 97.01

Haploinsufficiency Scores

• pHI: 0.0849
• hipred: N
• hipred_score: 0.112
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0509

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