ZNF25

zinc finger protein 25, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 10:37949572-37976647

Links

ENSG00000175395 ∙ NCBI:219749 ∙ OMIM:194528 ∙ HGNC:13043 ∙ Uniprot:P17030 ∙ 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 ZNF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF25 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in ZNF25

This is a list of pathogenic ClinVar variants found in the ZNF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-37952135-C-G		not specified	Uncertain significance (Mar 20, 2024)
10-37952171-C-A		not specified	Uncertain significance (Sep 22, 2023)
10-37952305-T-A		not specified	Uncertain significance (Apr 18, 2023)
10-37952306-A-G		not specified	Uncertain significance (Aug 16, 2021)
10-37952372-C-T		not specified	Uncertain significance (Mar 07, 2024)
10-37952389-T-C		not specified	Uncertain significance (Jun 11, 2021)
10-37952399-C-T		not specified	Uncertain significance (Jun 17, 2024)
10-37952421-T-A		not specified	Uncertain significance (Aug 01, 2023)
10-37952497-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-37952540-T-C		not specified	Likely benign (Mar 12, 2024)
10-37952598-G-C		not specified	Uncertain significance (Aug 17, 2021)
10-37952698-A-G		not specified	Uncertain significance (Feb 22, 2023)
10-37952969-T-C		not specified	Uncertain significance (Aug 02, 2021)
10-37952977-T-C		not specified	Uncertain significance (Sep 01, 2021)
10-37957032-G-A		not specified	Uncertain significance (Jul 20, 2022)
10-37957057-C-A		not specified	Uncertain significance (Feb 02, 2024)
10-37957083-T-C		not specified	Uncertain significance (Sep 27, 2022)
10-37957498-A-G		not specified	Uncertain significance (Oct 06, 2022)
10-37971709-T-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF25	protein_coding	protein_coding	ENST00000302609	5	27062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000408	0.960	125521	1	225	125747	0.000899

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	237	231	1.03	0.0000103	3038
Missense in Polyphen		118	105.36	1.12		1391
Synonymous	0.224	80	82.6	0.969	0.00000375	768
Loss of Function	1.87	10	18.7	0.534	8.67e-7	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000529	0.000528
Ashkenazi Jewish	0.00516	0.00517
East Asian	0.000489	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000489	0.000489
South Asian	0.00373	0.00370
Other	0.000817	0.000815

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: 0.0928

Intolerance Scores

• loftool: 0.757
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.247
• hipred: N
• hipred_score: 0.172
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp9

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