ZCCHC2

zinc finger CCHC-type containing 2, the group of Zinc fingers CCHC-type

Basic information

Region (hg38): 18:62523025-62587709

Previous symbols: [ "C18orf49" ]

Links

ENSG00000141664 ∙ NCBI:54877 ∙ OMIM:620095 ∙ HGNC:22916 ∙ Uniprot:Q9C0B9 ∙ 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 ZCCHC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC2 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				2		2
missense			117	7		124
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	118	9	0

Variants in ZCCHC2

This is a list of pathogenic ClinVar variants found in the ZCCHC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-62523455-A-G		not specified	Uncertain significance (Jul 09, 2021)
18-62523461-C-G		not specified	Uncertain significance (Jan 04, 2024)
18-62523471-C-T		not specified	Uncertain significance (Sep 14, 2022)
18-62523473-C-T		not specified	Uncertain significance (Feb 07, 2023)
18-62523490-G-T		not specified	Uncertain significance (Apr 08, 2024)
18-62523491-C-T		not specified	Uncertain significance (Nov 13, 2023)
18-62523497-G-T		not specified	Likely benign (Oct 12, 2021)
18-62523501-A-C		not specified	Uncertain significance (Oct 16, 2024)
18-62523502-C-G		not specified	Uncertain significance (Jun 30, 2022)
18-62523516-C-T		not specified	Uncertain significance (Nov 10, 2024)
18-62523518-A-G		not specified	Uncertain significance (Nov 07, 2022)
18-62523519-A-C		not specified	Uncertain significance (Nov 07, 2022)
18-62523527-T-C		not specified	Uncertain significance (Feb 22, 2023)
18-62523527-T-G		not specified	Uncertain significance (Dec 16, 2023)
18-62523581-C-T		not specified	Uncertain significance (Dec 12, 2023)
18-62523594-C-T		not specified	Uncertain significance (May 03, 2023)
18-62523600-C-G		not specified	Likely benign (Aug 17, 2021)
18-62523606-C-T		not specified	Uncertain significance (Aug 04, 2024)
18-62523615-C-T		not specified	Uncertain significance (Aug 23, 2021)
18-62523618-G-A		not specified	Uncertain significance (Nov 13, 2024)
18-62523635-G-A		not specified	Uncertain significance (Jun 21, 2023)
18-62523647-G-C		not specified	Uncertain significance (Jan 26, 2022)
18-62523648-C-G			Likely benign (Mar 01, 2022)
18-62523648-C-T		not specified	Uncertain significance (Jul 07, 2024)
18-62523663-G-A		not specified	Uncertain significance (Dec 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC2	protein_coding	protein_coding	ENST00000269499	14	64703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00624	124612	0	40	124652	0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.447	516	545	0.946	0.0000271	7511
Missense in Polyphen		159	199.61	0.79654		2676
Synonymous	-1.50	250	222	1.13	0.0000124	2462
Loss of Function	5.11	6	41.6	0.144	0.00000219	540

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00287	0.00279
East Asian	0.000113	0.000111
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.0000713	0.0000708
Middle Eastern	0.000113	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.493
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.68

Haploinsufficiency Scores

• pHI: 0.433
• hipred: N
• hipred_score: 0.422
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc2

Gene ontology

• Cellular component: cytoplasm
• Molecular function: nucleic acid binding;zinc ion binding;phosphatidylinositol binding