ZCCHC10

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

Basic information

Region (hg38): 5:132996984-133026604

Links

ENSG00000155329 ∙ NCBI:54819 ∙ ∙ HGNC:25954 ∙ Uniprot:Q8TBK6 ∙ 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 ZCCHC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC10 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in ZCCHC10

This is a list of pathogenic ClinVar variants found in the ZCCHC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132998647-C-T		not specified	Uncertain significance (May 12, 2024)
5-132998771-A-G		not specified	Uncertain significance (Feb 05, 2024)
5-132998782-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-133006881-C-G		not specified	Uncertain significance (Nov 03, 2022)
5-133026507-G-A		not specified	Uncertain significance (Oct 12, 2022)
5-133026510-C-A		not specified	Uncertain significance (Oct 27, 2022)
5-133026510-C-G		not specified	Uncertain significance (Feb 28, 2024)
5-133026518-C-G		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC10	protein_coding	protein_coding	ENST00000324170	4	29620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0597	0.875	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0176	83	82.6	1.01	0.00000358	1116
Missense in Polyphen		6	7.0976	0.84536		92
Synonymous	-0.000386	31	31.0	1.00	0.00000144	312
Loss of Function	1.55	3	7.60	0.395	3.25e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.678
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc10

Gene ontology

• Molecular function: nucleic acid binding;protein binding;zinc ion binding