ZCCHC13

zinc finger CCHC-type containing 13, the group of Zinc fingers CCHC-type

Basic information

Region (hg38): X:74304180-74305034

Links

ENSG00000187969 ∙ NCBI:389874 ∙ ∙ HGNC:31749 ∙ Uniprot:Q8WW36 ∙ 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 ZCCHC13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC13 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			13		1	14
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	13	0	3

Variants in ZCCHC13

This is a list of pathogenic ClinVar variants found in the ZCCHC13 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-74304271-G-T		not specified	Uncertain significance (Feb 22, 2025)
X-74304273-A-G		not specified	Uncertain significance (Sep 06, 2022)
X-74304275-TAA-T		ZCCHC13-related disorder	Likely benign (May 27, 2022)
X-74304290-G-T		ZCCHC13-related disorder	Likely benign (May 21, 2019)
X-74304311-G-A			Benign (Dec 04, 2017)
X-74304322-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-74304363-G-A		not specified	Uncertain significance (Mar 07, 2025)
X-74304369-G-A		ZCCHC13-related disorder	Benign (Jul 31, 2017)
X-74304444-T-C		not specified	Uncertain significance (Jan 20, 2025)
X-74304513-C-T		not specified	Uncertain significance (Jul 20, 2021)
X-74304529-G-A		not specified	Uncertain significance (Aug 12, 2021)
X-74304544-C-A		not specified	Uncertain significance (Apr 26, 2023)
X-74304567-G-A		not specified	Uncertain significance (Feb 24, 2025)
X-74304579-G-A		not specified	Uncertain significance (Oct 12, 2022)
X-74304616-A-G		not specified	Uncertain significance (Nov 08, 2022)
X-74304625-A-C		not specified	Uncertain significance (Oct 08, 2024)
X-74304643-C-T		not specified	Uncertain significance (Jul 19, 2023)
X-74304646-A-G		not specified	Uncertain significance (Sep 20, 2023)
X-74304654-T-C		not specified	Uncertain significance (Aug 09, 2021)
X-74304669-G-A		not specified	Uncertain significance (Sep 13, 2023)
X-74304722-A-G			Benign (Apr 06, 2018)
X-74304745-C-G		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC13	protein_coding	protein_coding	ENST00000339534	1	844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00139	0.443	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.712	62	79.9	0.776	0.00000716	1070
Missense in Polyphen		15	24.196	0.61995		369
Synonymous	0.589	28	32.3	0.868	0.00000308	333
Loss of Function	-0.104	4	3.78	1.06	3.95e-7	56

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.95

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc13
• Phenotype: normal phenotype

Gene ontology

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