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.

• not_specified (83 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_001007248.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			78	6		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	6	0

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