ZC3H13

zinc finger CCCH-type containing 13, the group of Zinc fingers CCCH-type|WTAP complex

Basic information

Region (hg38): 13:45954465-46052759

Previous symbols: [ "KIAA0853" ]

Links

ENSG00000123200 ∙ NCBI:23091 ∙ OMIM:616453 ∙ HGNC:20368 ∙ Uniprot:Q5T200 ∙ 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 ZC3H13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H13 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
missense			91	1		92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	91	3	0

Variants in ZC3H13

This is a list of pathogenic ClinVar variants found in the ZC3H13 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-45963901-C-T		not specified	Uncertain significance (Feb 07, 2023)
13-45963953-A-C		not specified	Uncertain significance (Jan 18, 2023)
13-45963983-G-T		not specified	Uncertain significance (Jan 03, 2022)
13-45964003-A-C		not specified	Uncertain significance (Aug 12, 2021)
13-45965312-C-A		not specified	Uncertain significance (Sep 14, 2022)
13-45965414-T-C		not specified	Uncertain significance (Dec 19, 2022)
13-45967589-C-G		not specified	Uncertain significance (Sep 01, 2021)
13-45967597-G-T		not specified	Uncertain significance (Sep 16, 2021)
13-45967615-T-C		not specified	Likely benign (May 15, 2024)
13-45967657-A-G		not specified	Uncertain significance (Dec 12, 2023)
13-45967702-T-C		not specified	Uncertain significance (Apr 23, 2024)
13-45967784-T-G		not specified	Uncertain significance (Jan 22, 2024)
13-45967812-T-C		not specified	Uncertain significance (Sep 21, 2021)
13-45967878-C-T		not specified	Uncertain significance (Feb 14, 2023)
13-45967911-T-C		not specified	Uncertain significance (May 05, 2023)
13-45967974-C-T		not specified	Uncertain significance (Dec 06, 2022)
13-45968769-G-A		not specified	Uncertain significance (Jun 10, 2024)
13-45968825-C-T		not specified	Uncertain significance (Mar 04, 2024)
13-45968924-C-T		not specified	Uncertain significance (Dec 02, 2021)
13-45968949-G-A		not specified	Uncertain significance (Aug 21, 2023)
13-45969000-T-G		not specified	Uncertain significance (May 26, 2024)
13-45969035-G-A		not specified	Uncertain significance (Nov 22, 2022)
13-45969050-A-G			Likely benign (Jan 01, 2023)
13-45969053-C-T		not specified	Uncertain significance (Dec 26, 2023)
13-45969087-T-C		not specified	Uncertain significance (Nov 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H13	protein_coding	protein_coding	ENST00000282007	16	98295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.72e-7	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	741	886	0.836	0.0000554	10227
Missense in Polyphen		67	87.769	0.76337		920
Synonymous	0.376	285	293	0.972	0.0000155	2984
Loss of Function	8.16	14	104	0.135	0.00000933	920

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs at the 3'- UTR (By similarity). Controls embryonic stem cells (ESCs) pluripotency via its role in m6A methylation (By similarity). In the WMM complex, anchors component of the MACOM subcomplex in the nucleus (By similarity). Also required for bridging WTAP to the RNA-binding component RBM15 (RBM15 or RBM15B) (By similarity). {ECO:0000250|UniProtKB:E9Q784}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.407
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35

Haploinsufficiency Scores

• pHI: 0.477
• hipred: Y
• hipred_score: 0.571
• ghis: 0.586

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h13

Gene ontology

• Biological process: mRNA processing;multicellular organism development;RNA splicing;mRNA methylation;regulation of stem cell population maintenance
• Cellular component: nucleoplasm;nuclear speck;RNA N6-methyladenosine methyltransferase complex
• Molecular function: RNA binding;protein binding;metal ion binding