ZNF596

zinc finger protein 596, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:232137-264703

Links

ENSG00000172748 ∙ NCBI:169270 ∙ ∙ HGNC:27268 ∙ Uniprot:Q8TC21 ∙ 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 ZNF596 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF596 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	4	0

Variants in ZNF596

This is a list of pathogenic ClinVar variants found in the ZNF596 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-242902-G-A		not specified	Uncertain significance (Jan 26, 2022)
8-243756-A-G			Likely benign (May 01, 2022)
8-243760-G-A		not specified	Uncertain significance (Jun 07, 2023)
8-243763-C-G		not specified	Uncertain significance (Apr 27, 2024)
8-244651-C-A		not specified	Uncertain significance (Mar 31, 2024)
8-245160-C-T		not specified	Uncertain significance (Apr 09, 2024)
8-245209-C-G		not specified	Uncertain significance (Jan 10, 2022)
8-245248-T-C		not specified	Uncertain significance (Aug 05, 2023)
8-245252-A-T		not specified	Uncertain significance (Dec 16, 2023)
8-245272-A-G		not specified	Uncertain significance (Nov 10, 2022)
8-245313-C-A		not specified	Uncertain significance (Jan 10, 2023)
8-245313-C-G		not specified	Uncertain significance (May 25, 2022)
8-245439-C-A		not specified	Uncertain significance (Mar 25, 2024)
8-245439-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-245440-G-A		not specified	Likely benign (Feb 12, 2024)
8-245470-C-G		not specified	Uncertain significance (Dec 15, 2022)
8-245563-G-A		not specified	Uncertain significance (Nov 05, 2021)
8-245578-C-T		not specified	Likely benign (Jan 23, 2023)
8-245643-C-G		not specified	Uncertain significance (Dec 18, 2023)
8-245658-A-T		not specified	Uncertain significance (Aug 05, 2023)
8-245668-C-G		not specified	Uncertain significance (May 27, 2022)
8-245671-G-C		not specified	Uncertain significance (Dec 08, 2023)
8-245673-G-C		not specified	Uncertain significance (Apr 28, 2022)
8-245895-C-A		not specified	Uncertain significance (Jul 20, 2021)
8-245907-G-A		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF596	protein_coding	protein_coding	ENST00000398612	5	15206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-13	0.0157	125593	0	151	125744	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.55	381	264	1.44	0.0000124	3358
Missense in Polyphen		132	92.313	1.4299		1191
Synonymous	-2.05	117	92.0	1.27	0.00000439	903
Loss of Function	-0.216	19	18.0	1.05	0.00000109	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000980	0.000979
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000628	0.000624
Middle Eastern	0.000980	0.000979
South Asian	0.000924	0.000915
Other	0.000163	0.000163

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: 0.992
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.148
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

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