ZC3H7A

zinc finger CCCH-type containing 7A, the group of Zinc fingers CCCH-type|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 16:11750586-11797258

Previous symbols: [ "ZC3HDC7", "ZC3H7" ]

Links

ENSG00000122299 ∙ NCBI:29066 ∙ OMIM:619819 ∙ HGNC:30959 ∙ Uniprot:Q8IWR0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZC3H7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H7A 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			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	43	1	0

Variants in ZC3H7A

This is a list of pathogenic ClinVar variants found in the ZC3H7A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11751380-G-C		not specified	Uncertain significance (Jul 27, 2022)
16-11751466-A-G		not specified	Uncertain significance (Feb 22, 2023)
16-11752765-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-11756259-G-A		not specified	Uncertain significance (Feb 16, 2023)
16-11756278-C-T		not specified	Uncertain significance (Dec 06, 2021)
16-11756290-T-C		not specified	Uncertain significance (Feb 11, 2022)
16-11756361-A-G		not specified	Uncertain significance (Apr 12, 2022)
16-11761467-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-11761474-T-C		not specified	Uncertain significance (May 30, 2024)
16-11761483-C-T		not specified	Uncertain significance (Nov 05, 2021)
16-11761501-C-G		not specified	Uncertain significance (Jun 03, 2022)
16-11762006-A-G		not specified	Uncertain significance (Sep 27, 2022)
16-11762025-T-C		not specified	Uncertain significance (May 05, 2023)
16-11765110-T-G		not specified	Uncertain significance (Jul 14, 2021)
16-11765530-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-11765563-C-T		not specified	Uncertain significance (Jan 31, 2024)
16-11765680-C-T		not specified	Uncertain significance (Sep 23, 2023)
16-11767461-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
16-11767494-A-G		not specified	Uncertain significance (Mar 18, 2024)
16-11767510-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-11767518-A-G		not specified	Uncertain significance (Aug 02, 2021)
16-11767549-C-G		not specified	Uncertain significance (Jul 05, 2023)
16-11768399-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-11768459-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-11769089-G-C		not specified	Uncertain significance (May 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H7A	protein_coding	protein_coding	ENST00000396516	22	46682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.74e-8	125734	0	8	125742	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	406	518	0.784	0.0000274	6428
Missense in Polyphen		89	202.12	0.44032		2432
Synonymous	-0.638	193	182	1.06	0.0000103	1707
Loss of Function	6.62	2	54.9	0.0364	0.00000277	715

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000442	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a specific regulator of miRNA biogenesis. Binds to microRNAs MIR7-1, MIR16-2 and MIR29A hairpins recognizing the 3'-ATA(A/T)-5' motif in the apical loop. {ECO:0000269|PubMed:28431233}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0927
• rvis_EVS: -0.39
• rvis_percentile_EVS: 27.03

Haploinsufficiency Scores

• pHI: 0.398
• hipred: Y
• hipred_score: 0.591
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h7a

Gene ontology

• Biological process: posttranscriptional regulation of gene expression;production of miRNAs involved in gene silencing by miRNA
• Cellular component: nucleus
• Molecular function: RNA binding;miRNA binding;metal ion binding