ZNF233

zinc finger protein 233, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:44259880-44275317

Links

ENSG00000159915 ∙ NCBI:353355 ∙ ∙ HGNC:30946 ∙ Uniprot:A6NK53 ∙ 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 ZNF233 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF233 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				1		1
missense			30	2		32
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	30	4	1

Variants in ZNF233

This is a list of pathogenic ClinVar variants found in the ZNF233 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44264365-C-A		not specified	Uncertain significance (Apr 26, 2023)
19-44266208-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-44266240-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-44266893-T-C		not specified	Uncertain significance (Mar 02, 2023)
19-44266923-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-44266930-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-44266956-G-C		not specified	Uncertain significance (Dec 16, 2023)
19-44267008-T-A			Likely benign (Apr 01, 2023)
19-44272920-T-C		not specified	Uncertain significance (Nov 10, 2022)
19-44272934-G-A			Likely benign (Jul 01, 2022)
19-44272936-A-C		not specified	Uncertain significance (Mar 07, 2023)
19-44272967-C-T		not specified	Uncertain significance (May 03, 2023)
19-44272971-T-C		not specified	Uncertain significance (Jan 03, 2024)
19-44272997-A-G		not specified	Uncertain significance (May 15, 2024)
19-44272998-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-44273248-T-A		not specified	Uncertain significance (May 27, 2022)
19-44273249-A-T		not specified	Uncertain significance (May 27, 2022)
19-44273344-C-A		not specified	Uncertain significance (Dec 14, 2023)
19-44273372-A-G		not specified	Uncertain significance (Oct 12, 2021)
19-44273436-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-44273533-C-T			Likely benign (Jul 01, 2022)
19-44273544-T-G		not specified	Uncertain significance (May 09, 2022)
19-44273569-G-C		not specified	Uncertain significance (May 13, 2024)
19-44273705-C-G		not specified	Uncertain significance (Dec 28, 2023)
19-44273705-C-T		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF233	protein_coding	protein_coding	ENST00000391958	4	25153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000187	0.487	125718	0	27	125745	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.368	323	342	0.944	0.0000154	4492
Missense in Polyphen		65	75.913	0.85624		1026
Synonymous	2.05	93	122	0.764	0.00000565	1145
Loss of Function	0.342	6	6.97	0.860	2.92e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000910	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000262	0.000261
Other	0.00	0.00

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: 0.902
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.38

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: N
• hipred_score: 0.112
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.455

Gene Damage Prediction

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

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;DNA-binding transcription factor activity;metal ion binding