ZC3H12C

zinc finger CCCH-type containing 12C, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 11:110093391-110171841

Links

ENSG00000149289 ∙ NCBI:85463 ∙ OMIM:615001 ∙ HGNC:29362 ∙ Uniprot:Q9C0D7 ∙ 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 ZC3H12C gene.

• Inborn genetic diseases (27 variants)
• X-linked Alport syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H12C 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in ZC3H12C

This is a list of pathogenic ClinVar variants found in the ZC3H12C region.

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

Position	Type	Phenotype	Significance	ClinVar
11-110093424-G-C		not specified	Uncertain significance (Aug 09, 2021)
11-110136669-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-110136723-C-T		not specified	Uncertain significance (Nov 07, 2022)
11-110136724-G-A		not specified	Likely benign (Aug 03, 2022)
11-110136760-A-G		not specified	Uncertain significance (Sep 12, 2023)
11-110136768-G-A		not specified	Likely benign (Jan 23, 2024)
11-110136886-A-G		not specified	Uncertain significance (Sep 19, 2022)
11-110136915-G-A		not specified	Uncertain significance (May 02, 2023)
11-110136981-A-G		not specified	Uncertain significance (Dec 16, 2023)
11-110136996-C-G		X-linked Alport syndrome	Uncertain significance (Jul 14, 2021)
11-110137018-T-C		not specified	Uncertain significance (Jan 27, 2022)
11-110137021-A-T		not specified	Uncertain significance (Nov 15, 2021)
11-110137023-C-T		not specified	Uncertain significance (Jun 16, 2023)
11-110137028-C-G		not specified	Uncertain significance (Jul 14, 2023)
11-110137039-G-T		not specified	Uncertain significance (May 09, 2023)
11-110137086-T-A		not specified	Uncertain significance (Jul 07, 2022)
11-110137110-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-110137120-G-A		not specified	Uncertain significance (Apr 22, 2022)
11-110137168-A-G		not specified	Uncertain significance (May 15, 2023)
11-110137353-G-T		not specified	Uncertain significance (Jul 08, 2021)
11-110137410-A-G		not specified	Uncertain significance (Oct 26, 2022)
11-110152933-A-C		not specified	Uncertain significance (Apr 13, 2022)
11-110159271-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-110159348-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-110159488-C-G		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H12C	protein_coding	protein_coding	ENST00000278590	6	78480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00162	124886	2	50	124938	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	377	489	0.771	0.0000268	5810
Missense in Polyphen		108	206.43	0.52317		2440
Synonymous	1.69	158	187	0.843	0.0000111	1694
Loss of Function	4.97	4	36.4	0.110	0.00000234	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000433	0.000432
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.000179	0.000165
Finnish	0.0000468	0.0000463
European (Non-Finnish)	0.000124	0.000124
Middle Eastern	0.000179	0.000165
South Asian	0.000752	0.000686
Other	0.000330	0.000329

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as RNase and regulate the levels of target RNA species. {ECO:0000305}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.402
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.699
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.318

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h12c

Gene ontology

• Biological process: biological_process;nucleic acid phosphodiester bond hydrolysis
• Cellular component: cellular_component
• Molecular function: molecular_function;endonuclease activity;metal ion binding