ZNF425

zinc finger protein 425, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:149102783-149126324

Links

ENSG00000204947 ∙ NCBI:155054 ∙ OMIM:619507 ∙ HGNC:20690 ∙ Uniprot:Q6IV72 ∙ 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 ZNF425 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF425 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			46	3		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	3	0

Variants in ZNF425

This is a list of pathogenic ClinVar variants found in the ZNF425 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-149103635-T-C		not specified	Uncertain significance (May 09, 2023)
7-149103647-C-A		not specified	Uncertain significance (Oct 02, 2023)
7-149103752-T-C		not specified	Uncertain significance (Apr 24, 2024)
7-149103777-C-G		not specified	Uncertain significance (Oct 03, 2022)
7-149103779-C-T		not specified	Uncertain significance (Aug 22, 2023)
7-149103844-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-149103950-C-A		not specified	Uncertain significance (Aug 04, 2023)
7-149103952-C-T		not specified	Uncertain significance (Aug 04, 2023)
7-149103958-A-G		not specified	Uncertain significance (Jan 05, 2022)
7-149103987-G-C		not specified	Uncertain significance (Sep 13, 2023)
7-149104013-G-T		not specified	Uncertain significance (May 18, 2023)
7-149104016-A-G		not specified	Uncertain significance (Jun 22, 2023)
7-149104024-T-C		not specified	Uncertain significance (Dec 14, 2021)
7-149104033-G-C		not specified	Uncertain significance (Feb 12, 2024)
7-149104073-G-A		not specified	Uncertain significance (Jul 19, 2022)
7-149104127-A-C		not specified	Uncertain significance (May 21, 2024)
7-149104148-T-A		not specified	Uncertain significance (Apr 21, 2022)
7-149104184-A-G		not specified	Uncertain significance (Aug 21, 2023)
7-149104207-T-C		not specified	Uncertain significance (Dec 26, 2023)
7-149104255-G-A		not specified	Uncertain significance (Dec 03, 2021)
7-149104274-G-A		not specified	Uncertain significance (Dec 15, 2023)
7-149104383-C-G		not specified	Uncertain significance (Jan 23, 2024)
7-149104451-C-T		not specified	Uncertain significance (Apr 01, 2024)
7-149104519-A-C		not specified	Uncertain significance (Oct 05, 2022)
7-149104528-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF425	protein_coding	protein_coding	ENST00000378061	4	23563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000332	0.369	125709	1	37	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	403	471	0.855	0.0000306	4994
Missense in Polyphen		120	127.64	0.94013		1514
Synonymous	-0.483	209	200	1.04	0.0000142	1370
Loss of Function	0.171	7	7.51	0.933	3.21e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000818	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000818	0.000816
South Asian	0.000564	0.000523
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. {ECO:0000269|PubMed:21266108}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.897
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.86

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.139
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.479

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