ZNF253

zinc finger protein 253, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:19865882-19894674

Previous symbols: [ "ZNF411" ]

Links

ENSG00000256771 ∙ NCBI:56242 ∙ OMIM:606954 ∙ HGNC:13497 ∙ Uniprot:O75346 ∙ 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 ZNF253 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF253 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	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	1

Variants in ZNF253

This is a list of pathogenic ClinVar variants found in the ZNF253 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19878545-C-G		not specified	Uncertain significance (Mar 10, 2025)
19-19878553-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-19878575-T-C		not specified	Uncertain significance (Mar 07, 2025)
19-19880104-C-A		not specified	Uncertain significance (Feb 27, 2023)
19-19880114-T-C		not specified	Uncertain significance (Aug 08, 2022)
19-19880132-T-C		not specified	Uncertain significance (Dec 06, 2022)
19-19891528-T-C		not specified	Uncertain significance (Nov 22, 2021)
19-19891537-G-T		not specified	Uncertain significance (Aug 28, 2023)
19-19891541-G-T		not specified	Uncertain significance (Aug 12, 2024)
19-19891549-G-C		not specified	Uncertain significance (Aug 12, 2021)
19-19891553-T-C			Likely benign (Mar 01, 2023)
19-19891617-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-19891666-A-C		not specified	Uncertain significance (Jan 30, 2024)
19-19891678-T-G		not specified	Uncertain significance (Apr 04, 2023)
19-19891738-C-T		not specified	Likely benign (Oct 16, 2023)
19-19891750-G-A		not specified	Uncertain significance (Apr 27, 2024)
19-19891764-A-G			Benign (Dec 13, 2017)
19-19891773-A-C		not specified	Uncertain significance (Jun 27, 2022)
19-19891780-G-A		not specified	Uncertain significance (Jan 01, 2025)
19-19891794-C-T		not specified	Uncertain significance (Nov 19, 2022)
19-19891812-A-G		not specified	Uncertain significance (Apr 15, 2022)
19-19891875-A-C		not specified	Uncertain significance (Feb 12, 2025)
19-19891900-A-C		not specified	Uncertain significance (Sep 10, 2024)
19-19891984-A-G		not specified	Uncertain significance (Nov 15, 2024)
19-19892028-T-A		not specified	Uncertain significance (Mar 11, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF253	protein_coding	protein_coding	ENST00000589717	4	28789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00321	0.619	125454	0	9	125463	0.0000359

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	231	257	0.900	0.0000117	3295
Missense in Polyphen		78	101.96	0.76504		1349
Synonymous	-0.373	92	87.6	1.05	0.00000406	886
Loss of Function	0.458	4	5.12	0.782	2.17e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.0000550	0.0000544
South Asian	0.00	0.00
Other	0.000172	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a transcription factor. Seem to have a transcriptional repression activity.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0899

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.112
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp65

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;zinc ion binding