ZC3H14

zinc finger CCCH-type containing 14, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 14:88562969-88627596

Links

ENSG00000100722 ∙ NCBI:79882 ∙ OMIM:613279 ∙ HGNC:20509 ∙ Uniprot:Q6PJT7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 56 (Limited), mode of inheritance: AD
• intellectual disability, autosomal recessive 56 (Limited), mode of inheritance: AR
• intellectual disability (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 56	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	21734151

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZC3H14 gene.

• Inborn genetic diseases (36 variants)
• not provided (33 variants)
• not specified (24 variants)
• Intellectual disability, autosomal recessive 56 (9 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H14 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	15	2	19
missense			35	3	1	39
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			19	2	5	26
Total	0	0	57	20	8

Variants in ZC3H14

This is a list of pathogenic ClinVar variants found in the ZC3H14 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-88563662-G-A		not specified	Likely benign (Jul 01, 2023)
14-88563665-G-A		ZC3H14-related disorder	Likely benign (Nov 05, 2019)
14-88563700-G-GT		not specified	Uncertain significance (Jun 04, 2018)
14-88563712-G-T		not specified	Uncertain significance (Jun 11, 2015)
14-88568112-G-C		ZC3H14-related disorder	Likely benign (Oct 23, 2020)
14-88568130-C-G		not specified	Uncertain significance (Mar 23, 2015)
14-88568148-C-T			Likely benign (Dec 31, 2019)
14-88571138-C-CATT			Likely benign (Aug 31, 2017)
14-88572044-A-G		not specified	Uncertain significance (Jun 22, 2021)
14-88572058-C-T		not specified	Likely benign (Mar 23, 2016)
14-88572076-C-T			Likely benign (Aug 08, 2018)
14-88572080-C-G			Benign (Sep 25, 2018)
14-88572088-C-T			Likely benign (Jul 01, 2018)
14-88572105-G-A		Intellectual disability, autosomal recessive 56	Uncertain significance (May 30, 2018)
14-88572162-G-A		not specified	Uncertain significance (Jul 27, 2022)
14-88572223-C-T		ZC3H14-related disorder	Likely benign (Oct 23, 2020)
14-88572575-T-C		not specified • Intellectual disability, autosomal recessive 56 • ZC3H14-related disorder	Benign/Likely benign (Jan 20, 2022)
14-88572585-T-C		not specified	Uncertain significance (Aug 28, 2023)
14-88572587-C-T			Likely benign (Oct 17, 2017)
14-88572606-C-T		Intellectual disability, autosomal recessive 56	Pathogenic (Dec 02, 2021)
14-88572780-A-G		not specified	Uncertain significance (Feb 07, 2023)
14-88572842-G-T		not specified	Uncertain significance (Dec 27, 2023)
14-88572860-G-A		ZC3H14-related disorder	Likely benign (May 07, 2019)
14-88572882-C-G		not specified	Uncertain significance (May 06, 2015)
14-88572890-T-C		not specified	Benign/Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H14	protein_coding	protein_coding	ENST00000251038	17	50601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.883	0.117	125617	0	131	125748	0.000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	317	399	0.795	0.0000206	4870
Missense in Polyphen		105	179.01	0.58656		2204
Synonymous	-1.80	166	139	1.19	0.00000761	1371
Loss of Function	4.88	8	42.2	0.189	0.00000245	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00578	0.00580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000599	0.000598
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in poly(A) tail length control in neuronal cells. Binds the polyadenosine RNA oligonucleotides. {ECO:0000269|PubMed:17630287, ECO:0000269|PubMed:24671764}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.0287
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.428
• hipred: Y
• hipred_score: 0.654
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h14
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of mRNA stability;negative regulation of mRNA polyadenylation
• Cellular component: nucleus;nucleolus;cytoplasm;nuclear speck;dendrite cytoplasm;axon cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding;poly(A) binding;metal ion binding