ZNF600

zinc finger protein 600, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52749942-52786807

Links

ENSG00000189190 ∙ NCBI:162966 ∙ ∙ HGNC:30951 ∙ Uniprot:Q6ZNG1 ∙ 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 ZNF600 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF600 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	4
missense			50	8	7	65
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	50	11	10

Variants in ZNF600

This is a list of pathogenic ClinVar variants found in the ZNF600 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52765595-G-A		not specified	Uncertain significance (May 20, 2024)
19-52765627-A-G		not specified	Uncertain significance (Oct 14, 2023)
19-52765637-A-G		not specified	Uncertain significance (Jun 03, 2022)
19-52765712-T-C		not specified	Uncertain significance (Dec 14, 2021)
19-52765714-A-T		not specified	Uncertain significance (Oct 27, 2022)
19-52765737-C-G			Benign (Oct 11, 2018)
19-52765748-C-A		not specified	Uncertain significance (Nov 08, 2022)
19-52765820-C-G		not specified	Likely benign (Dec 19, 2022)
19-52765820-CTT-C			Likely benign (Apr 19, 2018)
19-52765832-T-C		not specified	Likely benign (Feb 06, 2024)
19-52765859-C-T		not specified	Likely benign (Dec 30, 2023)
19-52765862-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-52765876-A-C		not specified	Uncertain significance (Sep 22, 2023)
19-52765884-T-G		not specified	Uncertain significance (Sep 22, 2023)
19-52765952-T-C		not specified	Uncertain significance (Apr 12, 2022)
19-52765991-T-C		not specified	Uncertain significance (Apr 29, 2024)
19-52766000-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-52766002-G-A		not specified	Uncertain significance (Apr 06, 2023)
19-52766038-C-T		not specified	Uncertain significance (Jul 13, 2021)
19-52766093-T-C		not specified	Uncertain significance (Mar 24, 2023)
19-52766114-G-T		not specified	Uncertain significance (Jun 02, 2023)
19-52766131-T-C		not specified	Uncertain significance (Nov 10, 2022)
19-52766198-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-52766205-G-A			Likely benign (Nov 01, 2023)
19-52766227-C-T		not specified	Likely benign (Mar 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF600	protein_coding	protein_coding	ENST00000338230	1	22597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.73	450	358	1.26	0.0000184	4794
Missense in Polyphen		138	124.07	1.1122		1814
Synonymous	-0.916	138	125	1.10	0.00000607	1268
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

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: 0.781
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.3

Haploinsufficiency Scores

• pHI: 0.900
• hipred: N
• hipred_score: 0.112
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

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