ZC3H12B

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

Basic information

Region (hg38): X:65034787-65507887

Previous symbols: [ "CXorf32" ]

Links

ENSG00000102053 ∙ NCBI:340554 ∙ OMIM:300889 ∙ HGNC:17407 ∙ Uniprot:Q5HYM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZC3H12B gene.

• Inborn genetic diseases (16 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H12B 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	1	3
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	2

Variants in ZC3H12B

This is a list of pathogenic ClinVar variants found in the ZC3H12B region.

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

Position	Type	Phenotype	Significance	ClinVar
X-65488859-G-A		not specified	Uncertain significance (Jul 20, 2021)
X-65488920-T-C		not specified	Uncertain significance (Dec 01, 2022)
X-65488953-T-C		not specified	Uncertain significance (Jan 30, 2024)
X-65488991-G-A		not specified	Uncertain significance (Jan 25, 2023)
X-65488991-G-T		not specified	Uncertain significance (Dec 06, 2022)
X-65489028-C-T		not specified	Uncertain significance (Dec 14, 2021)
X-65489064-G-A		not specified	Likely benign (May 16, 2022)
X-65489127-A-G			Benign (May 18, 2018)
X-65502074-C-T		not specified	Uncertain significance (Jan 03, 2024)
X-65502090-G-A			Benign (Jul 16, 2018)
X-65502120-C-G		not specified	Uncertain significance (Jan 04, 2024)
X-65502128-C-T		not specified	Uncertain significance (Oct 06, 2021)
X-65502304-A-C		not specified	Uncertain significance (Nov 09, 2023)
X-65502428-G-A		not specified	Uncertain significance (Jun 03, 2022)
X-65502454-C-T		not specified	Uncertain significance (May 25, 2022)
X-65502532-G-A		not specified	Uncertain significance (Oct 27, 2023)
X-65502568-C-G		not specified	Uncertain significance (Jun 29, 2023)
X-65502583-C-T		not specified	Likely benign (Dec 20, 2021)
X-65502623-A-G		not specified	Uncertain significance (Oct 05, 2023)
X-65502631-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-65502817-T-C		not specified	Uncertain significance (Feb 08, 2023)
X-65502845-G-A		not specified	Uncertain significance (Oct 26, 2022)
X-65502852-A-G			Likely benign (Feb 01, 2023)
X-65502914-C-T		not specified	Uncertain significance (Dec 14, 2021)
X-65503035-G-A		not specified	Uncertain significance (Apr 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H12B	protein_coding	protein_coding	ENST00000338957	5	19153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00165	124558	2	4	124564	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	204	335	0.609	0.0000263	5548
Missense in Polyphen		49	128.39	0.38166		2085
Synonymous	0.953	105	118	0.889	0.00000854	1614
Loss of Function	4.26	1	23.1	0.0433	0.00000208	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000157	0.000138
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000753	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000251	0.0000177
Middle Eastern	0.0000753	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• loftool: 0.252
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.768
• ghis: 0.648

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: Zc3h12b

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis
• Molecular function: endonuclease activity;metal ion binding