ZNF592

zinc finger protein 592, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 15:84748591-84806445

Previous symbols: [ "SCAR5" ]

Links

ENSG00000166716 ∙ NCBI:9640 ∙ OMIM:613624 ∙ HGNC:28986 ∙ Uniprot:Q92610 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 5	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic	12030328; 20531441

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF592 gene.

• Inborn genetic diseases (57 variants)
• not provided (11 variants)
• not specified (4 variants)
• Galloway-Mowat syndrome 1 (4 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF592 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	2	2	5
missense			54	6	4	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	55	8	8

Variants in ZNF592

This is a list of pathogenic ClinVar variants found in the ZNF592 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-84782760-G-C		not specified	Uncertain significance (Jan 23, 2024)
15-84782793-C-T		not specified	Uncertain significance (Jan 10, 2022)
15-84782844-T-G		not specified	Uncertain significance (Jan 27, 2022)
15-84782857-C-T		not specified	Uncertain significance (Mar 04, 2024)
15-84782858-C-T			Likely benign (Jul 01, 2022)
15-84782866-C-T		not specified	Uncertain significance (Jul 08, 2022)
15-84782931-A-G		not specified	Uncertain significance (Apr 04, 2023)
15-84782941-G-A		not specified	Uncertain significance (Aug 02, 2021)
15-84782953-A-G		not specified	Uncertain significance (Jul 11, 2023)
15-84782967-T-C		not specified	Likely benign (Aug 04, 2023)
15-84783054-C-A		ZNF592-related disorder	Benign (Jun 27, 2019)
15-84783082-C-G		not specified	Uncertain significance (Apr 14, 2022)
15-84783139-A-G		not specified	Uncertain significance (Mar 01, 2024)
15-84783143-C-T		ZNF592-related disorder	Likely benign (Feb 21, 2019)
15-84783144-G-A		not specified	Uncertain significance (Nov 03, 2023)
15-84783159-C-T		not specified	Uncertain significance (Dec 07, 2021)
15-84783189-C-A		not specified	Uncertain significance (Jan 26, 2022)
15-84783190-C-G		not specified	Uncertain significance (Jul 14, 2021)
15-84783190-C-T		not specified	Uncertain significance (Apr 08, 2022)
15-84783201-G-A		not specified	Uncertain significance (Aug 04, 2021)
15-84783244-C-T		not specified	Uncertain significance (Apr 09, 2022)
15-84783280-A-G		not specified	Uncertain significance (Feb 05, 2024)
15-84783289-C-T		not specified	Uncertain significance (May 31, 2023)
15-84783294-C-G		not specified	Uncertain significance (Aug 08, 2022)
15-84783339-G-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF592	protein_coding	protein_coding	ENST00000299927	8	57794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000155	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.804	651	711	0.915	0.0000437	8336
Missense in Polyphen		239	327.06	0.73076		3996
Synonymous	-1.44	324	293	1.11	0.0000190	2562
Loss of Function	5.37	1	35.6	0.0281	0.00000188	466

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	0.0000462	0.0000462
European (Non-Finnish)	0.0000444	0.0000439
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.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.00930
• rvis_EVS: -1.83
• rvis_percentile_EVS: 2.09

Haploinsufficiency Scores

• pHI: 0.335
• hipred: Y
• hipred_score: 0.580
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp592

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