ZCCHC18

zinc finger CCHC-type containing 18, the group of Zinc fingers CCHC-type|Paraneoplastic Ma antigens

Basic information

Region (hg38): X:104112131-104115842

Links

ENSG00000166707 ∙ NCBI:644353 ∙ ∙ HGNC:32459 ∙ Uniprot:P0CG32 ∙ 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 ZCCHC18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC18 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in ZCCHC18

This is a list of pathogenic ClinVar variants found in the ZCCHC18 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-104114119-G-C		not specified	Uncertain significance (Mar 04, 2024)
X-104114197-T-C		not specified	Uncertain significance (Apr 13, 2022)
X-104114240-A-C		not specified	Uncertain significance (Jan 31, 2024)
X-104114544-G-T		not specified	Uncertain significance (Dec 06, 2022)
X-104114623-A-C		not specified	Uncertain significance (Jun 29, 2023)
X-104114677-G-A		not specified	Uncertain significance (Jul 09, 2021)
X-104114718-C-A		not specified	Uncertain significance (Jan 30, 2024)
X-104114744-G-C		not specified	Uncertain significance (Dec 06, 2023)
X-104114796-C-T		not specified	Uncertain significance (Aug 16, 2022)
X-104114848-T-C		not specified	Uncertain significance (Mar 07, 2024)
X-104114941-A-C		not specified	Uncertain significance (Mar 15, 2024)
X-104114955-G-T		not specified	Uncertain significance (Jul 15, 2021)
X-104114974-C-T		not specified	Uncertain significance (Nov 23, 2021)
X-104115002-C-T			Likely benign (Mar 01, 2022)
X-104115069-T-C		not specified	Uncertain significance (Oct 03, 2023)
X-104115078-A-G			Likely benign (-)
X-104115082-G-A		not specified	Uncertain significance (Mar 23, 2022)
X-104115198-G-A		not specified	Uncertain significance (May 02, 2024)
X-104115267-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC18	protein_coding	protein_coding	ENST00000537356	1	3712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.413	0.554	125433	100	90	125623	0.000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.747	132	158	0.833	0.0000122	2644
Missense in Polyphen		28	29.423	0.95165		674
Synonymous	1.01	49	58.8	0.833	0.00000425	808
Loss of Function	1.70	1	5.18	0.193	3.25e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00230	0.00180
Ashkenazi Jewish	0.00	0.00
East Asian	0.000292	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.0000792
Middle Eastern	0.000292	0.000218
South Asian	0.00751	0.00468
Other	0.000666	0.000490

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc18

Gene ontology

• Molecular function: metal ion binding