ZC3H14

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

Basic information

Region (hg38): 14:88562970-88627596

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.

not_specified (92 variants)
not_provided (34 variants)
ZC3H14-related_disorder (10 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. These statistics are base on transcript: NM_000024824.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	21 clinvar	2 clinvar	25
missense			74 clinvar	8 clinvar	1 clinvar	83
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	29	3

Loading clinvar variants...

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