ZC2HC1C

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

Basic information

Region (hg38): 14:75064108-75119502

Previous symbols: [ "C14orf140", "FAM164C" ]

Links

ENSG00000119703 ∙ NCBI:79696 ∙ ∙ HGNC:20354 ∙ Uniprot:Q53FD0 ∙ 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 ZC2HC1C gene.

• Inborn genetic diseases (44 variants)
• not provided (39 variants)
• Arthrogryposis, Perthes disease, and upward gaze palsy (5 variants)
• NEK9-related lethal skeletal dysplasia (2 variants)
• - (2 variants)
• NEK9-related lethal skeletal dysplasia;Arthrogryposis, Perthes disease, and upward gaze palsy (2 variants)
• Goldberg-Shprintzen megacolon syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC2HC1C 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						0
missense			10	5		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	6	9	31	5	24	75
Total	6	9	41	10	24

Highest pathogenic variant AF is 0.000296

Variants in ZC2HC1C

This is a list of pathogenic ClinVar variants found in the ZC2HC1C region.

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

Position	Type	Phenotype	Significance	ClinVar
14-75070806-C-T		not specified	Uncertain significance (Dec 28, 2022)
14-75070815-G-A		not specified	Likely benign (Aug 16, 2021)
14-75070841-G-A		not specified	Uncertain significance (Mar 29, 2023)
14-75070965-A-T		not specified	Uncertain significance (Jun 09, 2022)
14-75070982-C-T		not specified	Uncertain significance (Oct 14, 2023)
14-75071076-C-A		not specified	Uncertain significance (Dec 30, 2023)
14-75071087-G-A		not specified	Uncertain significance (Jan 24, 2024)
14-75071177-G-A		not specified	Likely benign (Apr 07, 2022)
14-75071236-G-C		not specified	Uncertain significance (Jun 13, 2023)
14-75071237-A-T		not specified	Uncertain significance (Jun 13, 2023)
14-75071378-C-T		not specified	Uncertain significance (Nov 09, 2021)
14-75071564-C-G		not specified	Uncertain significance (Jan 29, 2024)
14-75071567-G-A		not specified	Uncertain significance (Mar 23, 2022)
14-75071610-C-T		not specified	Likely benign (Apr 26, 2023)
14-75071612-G-A		not specified	Likely benign (Sep 16, 2021)
14-75071714-G-A		not specified	Uncertain significance (Apr 07, 2023)
14-75071721-T-C		not specified	Likely benign (Dec 02, 2022)
14-75071724-A-T		not specified	Uncertain significance (Aug 23, 2021)
14-75071807-A-G		not specified	Uncertain significance (Jan 06, 2023)
14-75071885-A-C		not specified	Uncertain significance (Aug 20, 2023)
14-75084551-C-T		Arthrogryposis, Perthes disease, and upward gaze palsy • NEK9-related lethal skeletal dysplasia	Benign (Sep 05, 2021)
14-75084618-T-G			Benign (Dec 31, 2019)
14-75084623-C-A		Inborn genetic diseases	Uncertain significance (Apr 21, 2022)
14-75084623-C-T		Inborn genetic diseases	Uncertain significance (Feb 07, 2023)
14-75084650-C-T		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC2HC1C	protein_coding	protein_coding	ENST00000524913	2	14254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-9	0.233	124239	0	4	124243	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0112	249	249	1.00	0.0000141	2994
Missense in Polyphen		57	49.619	1.1488		636
Synonymous	0.165	100	102	0.979	0.00000608	891
Loss of Function	0.605	15	17.8	0.845	0.00000110	190

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	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0567

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.0212
• hipred: N
• hipred_score: 0.123
• ghis: 0.450

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: Zc2hc1c

Gene ontology

• Molecular function: protein binding;metal ion binding