ZC3H12D

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

Basic information

Region (hg38): 6:149446794-149485014

Previous symbols: [ "C6orf95" ]

Links

ENSG00000178199 ∙ NCBI:340152 ∙ OMIM:611106 ∙ HGNC:21175 ∙ Uniprot:A2A288 ∙ 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 ZC3H12D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H12D 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			36	4	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	6	1

Variants in ZC3H12D

This is a list of pathogenic ClinVar variants found in the ZC3H12D region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149450688-G-T		not specified	Uncertain significance (May 20, 2024)
6-149450708-G-T		not specified	Uncertain significance (Oct 10, 2023)
6-149450709-C-T		not specified	Uncertain significance (Oct 10, 2023)
6-149450762-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-149450773-C-T		not specified	Uncertain significance (May 13, 2024)
6-149450795-C-G		not specified	Likely benign (Jan 23, 2023)
6-149450806-G-T		not specified	Uncertain significance (Sep 01, 2021)
6-149450874-G-A		not specified	Uncertain significance (Jul 12, 2022)
6-149450900-G-A		not specified	Uncertain significance (May 31, 2023)
6-149450902-C-T			Likely benign (Jul 17, 2018)
6-149450914-G-C			Likely benign (Dec 01, 2022)
6-149450965-G-C		not specified	Uncertain significance (Dec 06, 2023)
6-149450969-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-149450998-G-C		not specified	Likely benign (Jan 19, 2022)
6-149451016-G-T		not specified	Uncertain significance (Jul 12, 2023)
6-149451027-G-C		not specified	Uncertain significance (Oct 20, 2023)
6-149451087-G-T		not specified	Uncertain significance (Oct 20, 2021)
6-149451133-C-A		not specified	Uncertain significance (Feb 28, 2024)
6-149451138-C-G		not specified	Uncertain significance (Aug 10, 2021)
6-149451152-C-A		not specified	Uncertain significance (Feb 05, 2024)
6-149451205-G-C		not specified	Uncertain significance (Oct 22, 2021)
6-149451228-A-T		not specified	Uncertain significance (Jul 25, 2023)
6-149451327-C-A		not specified	Uncertain significance (Mar 20, 2023)
6-149452669-A-T		not specified	Uncertain significance (Sep 20, 2023)
6-149452693-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H12D	protein_coding	protein_coding	ENST00000409806	5	37404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.156	0.830	124633	0	9	124642	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	203	268	0.759	0.0000167	3316
Missense in Polyphen		57	101.44	0.56193		1115
Synonymous	2.75	83	122	0.683	0.00000824	1144
Loss of Function	2.11	3	10.3	0.291	5.10e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000152
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate cell growth likely by suppressing RB1 phosphorylation (PubMed:19531561). May function as RNase and regulate the levels of target RNA species (Potential). In association with ZC3H12A enhances the degradation of interleukin IL-6 mRNA level in activated macrophages (PubMed:26134560). Serve as a tumor suppressor in certain leukemia cells (PubMed:17210687). Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation (PubMed:19531561). {ECO:0000269|PubMed:17210687, ECO:0000269|PubMed:19531561, ECO:0000269|PubMed:26134560, ECO:0000305}.
• Disease: DISEASE: Note=A chromosomal aberration involving ZC3H12D may be the cause of the transformation of follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL). Translocation t(2;6)(p12;q25) with IGK. Resulting protein may not be expressed.

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.0520
• hipred: Y
• hipred_score: 0.516
• ghis: 0.426

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.384

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h12d
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: 3'-UTR-mediated mRNA destabilization;nucleic acid phosphodiester bond hydrolysis
• Cellular component: P-body;nucleoplasm;cytoplasmic ribonucleoprotein granule
• Molecular function: endonuclease activity;protein binding;metal ion binding