ZNF598

zinc finger protein 598, E3 ubiquitin ligase, the group of Zinc fingers C2H2-type|Ring finger proteins

Basic information

Region (hg38): 16:1997654-2009821

Links

ENSG00000167962 ∙ NCBI:90850 ∙ OMIM:617508 ∙ HGNC:28079 ∙ Uniprot:Q86UK7 ∙ 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 ZNF598 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF598 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				2		2
missense			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	26	5	0

Variants in ZNF598

This is a list of pathogenic ClinVar variants found in the ZNF598 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1998452-G-A		not specified	Uncertain significance (Sep 22, 2023)
16-1998546-C-T		not specified	Uncertain significance (Apr 24, 2023)
16-1998572-G-A		not specified	Uncertain significance (May 27, 2022)
16-1998725-T-C		not specified	Uncertain significance (Jul 08, 2022)
16-1998977-G-A		not specified	Uncertain significance (Mar 30, 2024)
16-1998986-G-A		not specified	Uncertain significance (Mar 28, 2022)
16-1998999-C-G		not specified	Uncertain significance (May 29, 2024)
16-1999022-A-G		not specified	Uncertain significance (May 31, 2023)
16-1999040-G-A		not specified	Uncertain significance (Feb 22, 2024)
16-1999044-G-A		not specified	Uncertain significance (Apr 26, 2023)
16-1999535-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-1999556-G-A		not specified	Uncertain significance (Mar 28, 2024)
16-1999630-G-A			Likely benign (Feb 01, 2023)
16-1999659-G-A			Likely benign (Dec 01, 2022)
16-1999730-G-A		not specified	Uncertain significance (Sep 07, 2022)
16-1999765-G-A		not specified	Uncertain significance (May 05, 2023)
16-1999768-C-T		not specified	Uncertain significance (Mar 07, 2024)
16-1999773-T-G		not specified	Uncertain significance (Nov 21, 2022)
16-1999834-G-C		not specified	Uncertain significance (Sep 27, 2022)
16-1999837-C-T		not specified	Uncertain significance (May 21, 2024)
16-1999852-C-G		not specified	Uncertain significance (Mar 01, 2023)
16-1999909-G-A		not specified	Likely benign (Feb 22, 2023)
16-1999991-G-C		not specified	Uncertain significance (Apr 07, 2023)
16-2000086-G-A		not specified	Uncertain significance (May 15, 2024)
16-2000111-C-T		not specified	Likely benign (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF598	protein_coding	protein_coding	ENST00000431526	14	12170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.548	0.452	124397	0	7	124404	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.924	590	530	1.11	0.0000373	5726
Missense in Polyphen		182	209.06	0.87055		2364
Synonymous	-4.48	319	232	1.37	0.0000175	1804
Loss of Function	4.19	7	32.9	0.213	0.00000165	393

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)	0.0000384	0.0000355
Middle Eastern	0.00	0.00
South Asian	0.000167	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that plays a key role in the ribosome quality control (RQC), a pathway that takes place when a ribosome has stalled during translation (PubMed:28065601, PubMed:28132843). Required for ribosomes to terminally stall during translation of poly(A) sequences by mediating monoubiquitination of 40S ribosomal protein RPS10/eS10, RPS20/uS10 and RPS3/uS3 (PubMed:28065601, PubMed:28132843). Stalling precludes synthesis of a long poly-lysine tail and initiates the RQC pathway to degrade the potentially detrimental aberrant nascent polypeptide (PubMed:28065601, PubMed:28132843). Also acts as a component of the 4EHP-GYF2 complex, a multiprotein complex that acts as a repressor of translation initiation (PubMed:22751931). {ECO:0000269|PubMed:22751931, ECO:0000269|PubMed:28065601, ECO:0000269|PubMed:28132843}.

Haploinsufficiency Scores

• pHI: 0.451
• hipred: N
• hipred_score: 0.492
• ghis: 0.589

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp598

Gene ontology

• Biological process: protein monoubiquitination;protein ubiquitination;rescue of stalled ribosome
• Molecular function: RNA binding;protein binding;ribosome binding;metal ion binding;ubiquitin protein ligase activity