ZNF583

zinc finger protein 583, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56397965-56436035

Links

ENSG00000198440 ∙ NCBI:147949 ∙ ∙ HGNC:26427 ∙ Uniprot:Q96ND8 ∙ 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 ZNF583 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF583 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in ZNF583

This is a list of pathogenic ClinVar variants found in the ZNF583 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56414035-A-G		not specified	Uncertain significance (Sep 01, 2021)
19-56414048-A-C		not specified	Uncertain significance (Aug 08, 2022)
19-56414350-T-C		not specified	Uncertain significance (Mar 16, 2024)
19-56414353-G-A		not specified	Likely benign (Dec 03, 2021)
19-56414405-T-C		not specified	Uncertain significance (Jun 02, 2023)
19-56423098-A-G		not specified	Uncertain significance (Mar 29, 2023)
19-56423115-G-T		not specified	Uncertain significance (Apr 27, 2024)
19-56423176-T-G		not specified	Uncertain significance (Nov 12, 2021)
19-56423185-G-C		not specified	Uncertain significance (Mar 20, 2023)
19-56423257-T-A		not specified	Uncertain significance (May 12, 2024)
19-56423362-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-56423521-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-56423650-A-T		not specified	Uncertain significance (Jan 18, 2022)
19-56423743-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-56423799-G-A		not specified	Uncertain significance (May 06, 2024)
19-56423803-G-T		not specified	Uncertain significance (Nov 05, 2021)
19-56423866-C-G		not specified	Uncertain significance (Aug 16, 2021)
19-56424196-T-C		not specified	Uncertain significance (Oct 22, 2021)
19-56424328-C-A		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF583	protein_coding	protein_coding	ENST00000333201	4	38070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00716	0.992	125700	0	33	125733	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	173	289	0.599	0.0000131	3797
Missense in Polyphen		64	148.25	0.4317		1896
Synonymous	-0.408	103	97.9	1.05	0.00000440	977
Loss of Function	2.98	8	23.6	0.338	0.00000108	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
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: 0.744
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.496
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zfp583

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