ZC2HC1A

zinc finger C2HC-type containing 1A, the group of Zinc fingers C2HC-type

Basic information

Region (hg38): 8:78666050-78719765

Previous symbols: [ "C8orf70", "FAM164A" ]

Links

ENSG00000104427 ∙ NCBI:51101 ∙ ∙ HGNC:24277 ∙ Uniprot:Q96GY0 ∙ 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 ZC2HC1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC2HC1A 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			25	1		26
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	2	0

Variants in ZC2HC1A

This is a list of pathogenic ClinVar variants found in the ZC2HC1A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-78666161-G-A		not specified	Uncertain significance (Jul 14, 2022)
8-78678605-C-T		not specified	Uncertain significance (Nov 08, 2022)
8-78678675-C-T		not specified	Uncertain significance (Sep 26, 2022)
8-78686500-A-G		not specified	Uncertain significance (Aug 02, 2023)
8-78686515-T-C		not specified	Uncertain significance (Dec 16, 2024)
8-78686519-T-C		not specified	Uncertain significance (May 04, 2023)
8-78686566-G-A		not specified	Uncertain significance (Sep 11, 2024)
8-78686584-C-T		not specified	Uncertain significance (Feb 27, 2023)
8-78689225-A-G		not specified	Uncertain significance (Sep 30, 2024)
8-78689230-C-A		not specified	Uncertain significance (Aug 27, 2024)
8-78689251-A-T			Uncertain significance (Aug 05, 2023)
8-78689273-A-G		not specified	Uncertain significance (Jan 28, 2025)
8-78689309-G-A		not specified	Uncertain significance (Jun 22, 2021)
8-78689315-G-C		not specified	Uncertain significance (Dec 09, 2023)
8-78689328-A-G			Likely benign (Sep 01, 2024)
8-78689342-C-T		not specified	Uncertain significance (May 09, 2022)
8-78689363-G-A		not specified	Uncertain significance (Oct 05, 2021)
8-78689371-G-C		not specified	Uncertain significance (Jun 22, 2023)
8-78697419-G-A		not specified	Uncertain significance (May 24, 2023)
8-78697419-G-T		not specified	Uncertain significance (May 06, 2024)
8-78697440-C-T		not specified	Uncertain significance (Oct 11, 2024)
8-78697444-G-T		not specified	Uncertain significance (Mar 06, 2025)
8-78697446-A-G		not specified	Uncertain significance (Aug 12, 2024)
8-78697468-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-78697483-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC2HC1A	protein_coding	protein_coding	ENST00000263849	9	53719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.690	125715	0	15	125730	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.409	151	166	0.911	0.00000801	2064
Missense in Polyphen		40	62.08	0.64433		809
Synonymous	-0.569	62	56.6	1.10	0.00000274	636
Loss of Function	2.93	4	17.0	0.235	9.00e-7	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000573	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000900	0.0000879
Middle Eastern	0.0000573	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.336
• hipred: Y
• hipred_score: 0.518
• ghis: 0.564

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: Zc2hc1a

Gene ontology

• Molecular function: protein binding;metal ion binding