ZCCHC14

zinc finger CCHC-type containing 14, the group of Sterile alpha motif domain containing|Zinc fingers CCHC-type

Basic information

Region (hg38): 16:87406245-87493024

Links

ENSG00000140948 ∙ NCBI:23174 ∙ ∙ HGNC:24134 ∙ Uniprot:Q8WYQ9 ∙ 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 ZCCHC14 gene.

• Inborn genetic diseases (50 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC14 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	4
missense			49	1	2	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	3	4

Variants in ZCCHC14

This is a list of pathogenic ClinVar variants found in the ZCCHC14 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-87411519-G-A		not specified	Uncertain significance (Feb 12, 2024)
16-87411577-G-A			Benign (Nov 26, 2018)
16-87411636-C-T		not specified	Uncertain significance (May 25, 2022)
16-87411641-C-A		not specified	Uncertain significance (Sep 27, 2022)
16-87411647-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-87411696-C-T		not specified	Uncertain significance (Apr 27, 2022)
16-87411704-G-A		not specified	Uncertain significance (Jul 20, 2021)
16-87411732-G-A		not specified	Uncertain significance (May 03, 2023)
16-87411765-C-G		not specified	Uncertain significance (Mar 01, 2024)
16-87411786-C-T		not specified	Uncertain significance (Dec 26, 2023)
16-87411804-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-87411811-G-A			Likely benign (Dec 01, 2023)
16-87411887-T-C		not specified	Uncertain significance (Nov 27, 2023)
16-87411909-C-A		not specified	Uncertain significance (May 25, 2022)
16-87411912-T-C		not specified	Uncertain significance (Jul 05, 2023)
16-87411926-C-T		not specified	Uncertain significance (May 25, 2022)
16-87411965-G-A		not specified	Uncertain significance (Aug 14, 2023)
16-87412034-G-A		not specified	Uncertain significance (Mar 02, 2023)
16-87412040-G-T		not specified	Uncertain significance (Jan 23, 2024)
16-87412066-G-T			Benign (Jun 20, 2018)
16-87412103-G-A		not specified	Uncertain significance (Feb 06, 2023)
16-87412145-G-A		not specified	Uncertain significance (May 17, 2023)
16-87412146-T-A		not specified	Uncertain significance (Nov 09, 2021)
16-87412193-G-C		not specified	Uncertain significance (Mar 23, 2022)
16-87412196-T-C		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC14	protein_coding	protein_coding	ENST00000268616	13	85800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0215	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.813	531	586	0.906	0.0000367	6164
Missense in Polyphen		99	154.93	0.63899		1763
Synonymous	-4.17	348	262	1.33	0.0000197	1961
Loss of Function	4.59	5	33.8	0.148	0.00000168	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000134	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000289	0.0000264
Middle Eastern	0.000134	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.146
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.17

Haploinsufficiency Scores

• pHI: 0.528
• hipred: Y
• hipred_score: 0.563
• ghis: 0.647

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Zcchc14
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

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