ZC3H10

zinc finger CCCH-type containing 10, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 12:56118260-56127514

Previous symbols: [ "ZC3HDC10" ]

Links

ENSG00000135482 ∙ NCBI:84872 ∙ ∙ HGNC:25893 ∙ Uniprot:Q96K80 ∙ 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 ZC3H10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H10 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			15			15
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in ZC3H10

This is a list of pathogenic ClinVar variants found in the ZC3H10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56120627-G-A		not specified	Uncertain significance (Jul 09, 2024)
12-56120632-G-A		not specified	Uncertain significance (Dec 10, 2024)
12-56120634-G-T		not specified	Uncertain significance (Jun 28, 2022)
12-56120726-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-56120791-A-G		not specified	Uncertain significance (Apr 18, 2023)
12-56120873-G-T		not specified	Uncertain significance (Aug 01, 2024)
12-56120983-C-T		not specified	Uncertain significance (Jul 20, 2022)
12-56121070-G-C		not specified	Uncertain significance (Dec 01, 2022)
12-56121077-G-T		not specified	Uncertain significance (Dec 17, 2023)
12-56121092-C-T		not specified	Uncertain significance (Jul 25, 2023)
12-56121094-A-G		not specified	Uncertain significance (Jul 15, 2024)
12-56121110-C-CAGGACGACGTCATGATCTCTATGAT			Uncertain significance (Jul 01, 2019)
12-56121118-C-T		not specified	Uncertain significance (Jun 25, 2024)
12-56121131-A-G		not specified	Uncertain significance (Sep 27, 2024)
12-56121143-A-C		not specified	Uncertain significance (Jul 09, 2024)
12-56121146-T-A		not specified	Uncertain significance (Mar 11, 2024)
12-56121187-C-T			Uncertain significance (Jul 01, 2019)
12-56121211-C-G		not specified	Uncertain significance (Dec 19, 2022)
12-56121211-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-56121233-C-T		not specified	Uncertain significance (Oct 10, 2023)
12-56121257-C-T		not specified	Uncertain significance (Jun 23, 2023)
12-56121260-G-A		not specified	Uncertain significance (Mar 30, 2024)
12-56121532-C-T		not specified	Uncertain significance (Aug 02, 2023)
12-56121583-C-T		not specified	Uncertain significance (Jun 26, 2023)
12-56121640-C-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H10	protein_coding	protein_coding	ENST00000257940	1	4336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.316	0.681	125741	0	3	125744	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	165	270	0.610	0.0000158	2789
Missense in Polyphen		29	69.175	0.41923		747
Synonymous	-1.17	117	102	1.15	0.00000555	957
Loss of Function	2.53	3	12.7	0.236	9.77e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0260
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.493
• hipred: Y
• hipred_score: 0.675
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h10

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;posttranscriptional regulation of gene expression;negative regulation of production of miRNAs involved in gene silencing by miRNA
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: RNA binding;protein binding;miRNA binding;metal ion binding