ZNF599

zinc finger protein 599, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:34758073-34773229

Links

ENSG00000153896 ∙ NCBI:148103 ∙ ∙ HGNC:26408 ∙ Uniprot:Q96NL3 ∙ 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 ZNF599 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF599 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			56	6		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	6	0

Variants in ZNF599

This is a list of pathogenic ClinVar variants found in the ZNF599 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34759056-C-T		not specified	Uncertain significance (Oct 27, 2022)
19-34759087-A-C		not specified	Uncertain significance (Jan 19, 2022)
19-34759095-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-34759131-T-C		not specified	Uncertain significance (Dec 07, 2024)
19-34759170-A-G		not specified	Uncertain significance (Sep 12, 2023)
19-34759213-T-C		not specified	Uncertain significance (Dec 15, 2023)
19-34759219-T-A		not specified	Uncertain significance (May 25, 2023)
19-34759230-C-T		not specified	Uncertain significance (Jul 16, 2024)
19-34759231-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-34759297-T-C		not specified	Uncertain significance (Jan 10, 2023)
19-34759309-T-A		not specified	Uncertain significance (May 04, 2022)
19-34759388-C-A		not specified	Uncertain significance (Dec 21, 2022)
19-34759398-C-T		not specified	Uncertain significance (Nov 08, 2021)
19-34759410-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-34759435-A-G		not specified	Uncertain significance (May 08, 2023)
19-34759475-C-G		not specified	Uncertain significance (Dec 15, 2021)
19-34759476-A-G		not specified	Uncertain significance (Aug 27, 2024)
19-34759479-T-A		not specified	Uncertain significance (Aug 19, 2024)
19-34759486-T-C		not specified	Uncertain significance (Nov 18, 2022)
19-34759529-C-G		not specified	Uncertain significance (Sep 08, 2024)
19-34759609-C-T		not specified	Likely benign (Feb 15, 2023)
19-34759648-G-C		not specified	Uncertain significance (Oct 04, 2024)
19-34759654-T-G		not specified	Uncertain significance (May 20, 2024)
19-34759662-G-A		not specified	Uncertain significance (May 31, 2023)
19-34759780-A-G		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF599	protein_coding	protein_coding	ENST00000329285	4	15154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.13e-7	0.894	120434	62	5252	125748	0.0214

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.128	319	313	1.02	0.0000160	3900
Missense in Polyphen		79	93.414	0.84569		1251
Synonymous	1.53	93	114	0.818	0.00000581	1072
Loss of Function	1.66	14	22.5	0.622	0.00000144	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0103	0.0103
Ashkenazi Jewish	0.0521	0.0518
East Asian	0.00136	0.00136
Finnish	0.0353	0.0352
European (Non-Finnish)	0.0234	0.0232
Middle Eastern	0.00136	0.00136
South Asian	0.0350	0.0347
Other	0.0171	0.0173

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: 0.877
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.97

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.112
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.537

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;protein binding;metal ion binding