ZC3H15

zinc finger CCCH-type containing 15, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 2:186486253-186511929

Links

ENSG00000065548 ∙ NCBI:55854 ∙ OMIM:619704 ∙ HGNC:29528 ∙ Uniprot:Q8WU90 ∙ 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 ZC3H15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H15 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in ZC3H15

This is a list of pathogenic ClinVar variants found in the ZC3H15 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-186486449-A-T		not specified	Uncertain significance (Oct 16, 2024)
2-186495288-A-G		not specified	Uncertain significance (Oct 18, 2021)
2-186495326-C-G		not specified	Uncertain significance (Jan 09, 2024)
2-186501334-T-G		not specified	Uncertain significance (May 26, 2022)
2-186501422-A-G		not specified	Uncertain significance (Nov 28, 2024)
2-186504134-C-G		not specified	Uncertain significance (Dec 28, 2022)
2-186504143-G-T		not specified	Uncertain significance (Apr 13, 2022)
2-186504157-T-A		not specified	Uncertain significance (Jan 02, 2024)
2-186504184-A-T		not specified	Uncertain significance (Oct 19, 2024)
2-186505524-A-G		not specified	Uncertain significance (Feb 20, 2025)
2-186505534-T-G		not specified	Uncertain significance (Sep 08, 2024)
2-186505580-G-A		not specified	Uncertain significance (Dec 15, 2022)
2-186505596-T-C		not specified	Uncertain significance (Nov 26, 2024)
2-186505768-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-186505825-G-A		not specified	Uncertain significance (May 02, 2024)
2-186506735-A-G		not specified	Uncertain significance (Jan 04, 2025)
2-186506758-A-C		not specified	Uncertain significance (May 14, 2024)
2-186506808-A-T		not specified	Uncertain significance (May 30, 2024)
2-186508614-G-A		not specified	Uncertain significance (Feb 13, 2024)
2-186508627-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-186508686-T-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H15	protein_coding	protein_coding	ENST00000337859	10	23208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.903	0.0974	124781	0	11	124792	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	136	211	0.645	0.0000103	2848
Missense in Polyphen		16	49.556	0.32287		743
Synonymous	0.264	68	70.8	0.960	0.00000347	715
Loss of Function	3.61	3	20.7	0.145	9.54e-7	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.0000550	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protects DRG1 from proteolytic degradation. {ECO:0000250}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.801
• hipred: Y
• hipred_score: 0.825
• ghis: 0.675

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h15

Gene ontology

• Biological process: cytoplasmic translation;regulation of transcription by RNA polymerase II;cytokine-mediated signaling pathway
• Cellular component: nucleolus;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA binding;protein binding;cadherin binding;metal ion binding