ZNF304

zinc finger protein 304, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57351271-57359898

Links

ENSG00000131845 ∙ NCBI:57343 ∙ OMIM:613840 ∙ HGNC:13505 ∙ Uniprot:Q9HCX3 ∙ 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 ZNF304 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF304 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			33	4		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	34	5	0

Variants in ZNF304

This is a list of pathogenic ClinVar variants found in the ZNF304 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57353740-G-A		not specified	Uncertain significance (Apr 28, 2022)
19-57353764-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-57353788-G-C		not specified	Uncertain significance (Nov 18, 2022)
19-57353845-A-T		not specified	Likely benign (Sep 14, 2021)
19-57356051-A-G		not specified	Uncertain significance (Jan 26, 2022)
19-57356075-T-C		not specified	Uncertain significance (Sep 22, 2023)
19-57356077-T-G		not specified	Uncertain significance (Jul 20, 2021)
19-57356258-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-57356311-G-A		not specified	Uncertain significance (Jun 29, 2023)
19-57356372-C-A		not specified	Uncertain significance (Dec 19, 2023)
19-57356372-C-T		not specified	Uncertain significance (Oct 11, 2021)
19-57356398-C-A		not specified	Uncertain significance (Dec 21, 2021)
19-57356405-G-T		not specified	Uncertain significance (Oct 10, 2023)
19-57356427-G-C		not specified	Uncertain significance (Oct 25, 2022)
19-57356441-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-57356443-G-A		not specified	Uncertain significance (May 06, 2022)
19-57356462-C-T		not specified	Uncertain significance (Oct 04, 2022)
19-57356519-A-G		not specified	Uncertain significance (Nov 22, 2023)
19-57356541-T-G		not specified	Uncertain significance (May 21, 2024)
19-57356545-G-A		not specified	Likely benign (Jan 18, 2022)
19-57356636-G-T		not specified	Uncertain significance (Apr 26, 2023)
19-57356645-T-C		not specified	Uncertain significance (Dec 21, 2023)
19-57356649-C-A		not specified	Uncertain significance (Nov 10, 2022)
19-57356674-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-57356678-G-A		not specified	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF304	protein_coding	protein_coding	ENST00000391705	3	8592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0329	0.965	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	278	359	0.774	0.0000178	4431
Missense in Polyphen		69	124.24	0.55536		1533
Synonymous	0.148	123	125	0.983	0.00000625	1180
Loss of Function	2.76	6	19.0	0.316	7.95e-7	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000426	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as transcriptional regulator and plays a role in gene silencing (PubMed:24623306, PubMed:26081979). Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of several tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) by inducing trimethylation of 'Lys-27' of histone H3 (H3K27me3) (PubMed:24623306) in a Polycomb group (PcG) complexes-dependent manner. Associates at promoter regions of TSGs and mediates the recruitment of the corepressor complex containing the scaffolding protein TRIM28, methyltransferase DNMT1 and histone methyltransferase SETDB1 and/or the PcG complexes at those sites (PubMed:24623306). Transcription factor involved in the metastatic cascade process by inducing cell migration and proliferation and gain resistance to anoikis of ovarian carcinoma (OC) cells via integrin-mediated signaling pathways (PubMed:26081979). Associates with the ITGB1 promoter and positively regulates beta-1 integrin transcription expression (PubMed:26081979). Promotes angiogenesis (PubMed:26081979). Promotes tumor growth (PubMed:24623306, PubMed:26081979). {ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:26081979}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.472
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.5

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.302
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0817

Gene Damage Prediction

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

Gene ontology

• Biological process: angiogenesis;chromatin organization;integrin-mediated signaling pathway;Ras protein signal transduction;positive regulation of cell migration;negative regulation of chromatin binding;positive regulation of angiogenesis;positive regulation of transcription by RNA polymerase II;positive regulation of epithelial cell proliferation;positive regulation of methylation-dependent chromatin silencing;positive regulation of histone H3-K9 trimethylation;positive regulation of histone H3-K27 trimethylation;negative regulation of anoikis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding;promoter-specific chromatin binding