ZNF256

zinc finger protein 256, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57940833-57947706

Links

ENSG00000152454 ∙ NCBI:10172 ∙ OMIM:606956 ∙ HGNC:13049 ∙ Uniprot:Q9Y2P7 ∙ 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 ZNF256 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF256 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			36	7		43
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	7	0

Variants in ZNF256

This is a list of pathogenic ClinVar variants found in the ZNF256 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57940938-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-57940983-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-57940995-A-G		not specified	Uncertain significance (Nov 12, 2021)
19-57941029-G-C		not specified	Uncertain significance (Feb 17, 2024)
19-57941034-T-C		not specified	Uncertain significance (Dec 09, 2023)
19-57941046-A-T		not specified	Uncertain significance (Mar 31, 2023)
19-57941102-T-C		not specified	Uncertain significance (Aug 02, 2022)
19-57941111-C-T		not specified	Likely benign (Jun 22, 2023)
19-57941121-C-T		not specified	Likely benign (Aug 20, 2023)
19-57941157-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-57941219-T-C		not specified	Uncertain significance (Feb 09, 2022)
19-57941222-C-G		not specified	Uncertain significance (Mar 01, 2023)
19-57941362-C-G		not specified	Uncertain significance (Aug 12, 2021)
19-57941457-T-G		not specified	Uncertain significance (Jan 31, 2025)
19-57941475-T-C		not specified	Uncertain significance (Aug 12, 2024)
19-57941516-C-G		not specified	Uncertain significance (Mar 09, 2025)
19-57941547-G-A		not specified	Uncertain significance (Oct 26, 2021)
19-57941564-A-G		not specified	Uncertain significance (Feb 04, 2025)
19-57941574-A-G		not specified	Uncertain significance (Feb 10, 2023)
19-57941612-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-57941615-C-T		not specified	Likely benign (Feb 21, 2024)
19-57941645-A-C		not specified	Uncertain significance (Nov 24, 2024)
19-57941818-T-A		not specified	Uncertain significance (Feb 20, 2025)
19-57941861-A-C		not specified	Uncertain significance (Mar 29, 2022)
19-57941898-A-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF256	protein_coding	protein_coding	ENST00000282308	3	6843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00553	0.496	125721	0	5	125726	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0604	322	319	1.01	0.0000159	4202
Missense in Polyphen		92	101.54	0.90601		1364
Synonymous	-1.01	128	114	1.12	0.00000589	1122
Loss of Function	-0.135	3	2.76	1.09	1.17e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that plays a role in cell proliferation. Requires TRIM28 for its activity. {ECO:0000269|PubMed:18060868}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0913

Intolerance Scores

• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.112
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

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;multicellular organism development;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding