ZNF589

zinc finger protein 589, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:48241100-48299253

Links

ENSG00000164048 ∙ NCBI:51385 ∙ OMIM:616702 ∙ HGNC:16747 ∙ Uniprot:Q86UQ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF589 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF589 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			15	1	3	19
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	1		11
Total	0	0	25	4	3

Variants in ZNF589

This is a list of pathogenic ClinVar variants found in the ZNF589 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48241178-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-48241205-A-G		ZNF589-related disorder	Benign (Oct 25, 2019)
3-48247686-G-A		ZNF589-related disorder	Benign (Jun 14, 2018)
3-48260816-C-A		not specified	Uncertain significance (Aug 08, 2023)
3-48260850-C-T		not specified	Uncertain significance (Aug 09, 2021)
3-48260927-C-T			Likely benign (May 17, 2018)
3-48267951-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-48267952-C-G		not specified	Uncertain significance (Feb 05, 2024)
3-48268118-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-48268128-G-T		not specified	Uncertain significance (May 09, 2023)
3-48268142-G-A		not specified	Uncertain significance (Dec 31, 2023)
3-48268163-A-T		not specified	Uncertain significance (Nov 18, 2023)
3-48268166-A-G		not specified	Uncertain significance (Jul 27, 2024)
3-48268230-G-T		not specified • ZNF589-related disorder	Uncertain significance (Feb 15, 2023)
3-48268290-T-C		not specified	Uncertain significance (Nov 13, 2024)
3-48268296-G-T		not specified	Uncertain significance (Nov 24, 2024)
3-48268310-G-A		not specified	Uncertain significance (Feb 06, 2023)
3-48268338-C-G		ZNF589-related disorder	Benign (Oct 25, 2019)
3-48268348-G-C		not specified	Uncertain significance (Dec 01, 2022)
3-48268454-C-T		ZNF589-related disorder	Likely benign (Dec 13, 2018)
3-48268455-G-C		not specified	Uncertain significance (Jul 30, 2024)
3-48268484-A-C		not specified	Uncertain significance (Dec 04, 2024)
3-48268515-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-48268526-G-A		not specified	Uncertain significance (Nov 13, 2023)
3-48268565-C-T		ZNF589-related disorder	Likely benign (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF589	protein_coding	protein_coding	ENST00000354698	4	58154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00492	0.709	125206	0	6	125212	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0571	191	193	0.988	0.00000952	2366
Missense in Polyphen		45	37.907	1.1871		488
Synonymous	0.760	66	74.3	0.888	0.00000380	707
Loss of Function	0.723	4	5.90	0.678	2.52e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000558	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in hematopoietic stem/progenitor cell differentiation. May play a role as a DNA binding-dependent transcriptional repressor. {ECO:0000269|PubMed:10029171, ECO:0000269|PubMed:12097288}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0820

Intolerance Scores

• loftool: 0.768
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.112
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

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
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;metal ion binding