ZC3H12B

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

Basic information

Region (hg38): X:65034788-65507887

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.

• not_specified (48 variants)
• not_provided (8 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. These statistics are base on transcript: NM_001010888.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			43	6	1	50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	8	2

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