ZNF254

zinc finger protein 254, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:24033405-24129968

Previous symbols: [ "ZNF91L", "ZNF539" ]

Links

ENSG00000213096 ∙ NCBI:9534 ∙ OMIM:604768 ∙ HGNC:13047 ∙ Uniprot:O75437 ∙ 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 ZNF254 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF254 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			61	1		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	61	1	0

Variants in ZNF254

This is a list of pathogenic ClinVar variants found in the ZNF254 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-24087327-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-24105979-C-G		not specified	Uncertain significance (Oct 25, 2022)
19-24106030-G-A		not specified	Uncertain significance (Jan 18, 2022)
19-24106054-C-G		not specified	Uncertain significance (May 23, 2023)
19-24106556-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-24106569-A-C		not specified	Uncertain significance (Feb 10, 2023)
19-24106571-C-G		not specified	Uncertain significance (Nov 20, 2023)
19-24106617-G-T		not specified	Uncertain significance (Nov 22, 2021)
19-24106640-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-24126271-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-24126275-A-G		not specified	Uncertain significance (Dec 05, 2022)
19-24126277-G-C		not specified	Uncertain significance (Feb 28, 2024)
19-24126379-A-G		not specified	Uncertain significance (May 02, 2024)
19-24126383-G-A		not specified	Uncertain significance (Jun 01, 2023)
19-24126405-C-G		not specified	Uncertain significance (Dec 15, 2023)
19-24126469-G-A		not specified	Uncertain significance (Sep 14, 2021)
19-24126529-A-G		not specified	Uncertain significance (Nov 17, 2022)
19-24126560-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-24126560-G-C		not specified	Uncertain significance (Dec 14, 2021)
19-24126578-T-C		not specified	Uncertain significance (Aug 30, 2022)
19-24126589-A-G		not specified	Uncertain significance (Aug 21, 2023)
19-24126616-A-G		not specified	Uncertain significance (Oct 06, 2021)
19-24126635-G-A		not specified	Uncertain significance (Nov 22, 2022)
19-24126641-A-C		not specified	Uncertain significance (Dec 13, 2021)
19-24126693-T-G		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF254	protein_coding	protein_coding	ENST00000357002	4	96379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000504	0.462	125696	0	17	125713	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.15	489	328	1.49	0.0000150	4319
Missense in Polyphen		65	52.69	1.2336		796
Synonymous	-2.68	147	111	1.32	0.00000499	1131
Loss of Function	0.143	5	5.36	0.933	2.27e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000985	0.0000653
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)

Recessive Scores

• pRec: 0.0746

Intolerance Scores

• loftool: 0.901
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.71

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.148
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0397

Gene Damage Prediction

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

Gene ontology

• Biological process: negative 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