ZC3H11A

zinc finger CCCH-type containing 11A, the group of Transcription and export complex 1 subunits|Zinc fingers CCCH-type

Basic information

Region (hg38): 1:203795623-203854999

Previous symbols: [ "ZC3HDC11A" ]

Links

ENSG00000058673 ∙ NCBI:9877 ∙ OMIM:613513 ∙ HGNC:29093 ∙ Uniprot:O75152 ∙ 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 ZC3H11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H11A 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				1	1	2
missense			40	5		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			39	4		43
Total	0	0	79	10	1

Variants in ZC3H11A

This is a list of pathogenic ClinVar variants found in the ZC3H11A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-203797619-A-G		not specified	Uncertain significance (Mar 07, 2023)
1-203797623-A-T		not specified	Uncertain significance (Feb 10, 2023)
1-203797643-G-T		not specified	Uncertain significance (Jul 02, 2024)
1-203797721-G-A		not specified	Uncertain significance (May 31, 2023)
1-203797746-G-A		not specified	Uncertain significance (May 30, 2023)
1-203797791-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-203797803-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-203797823-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-203797998-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-203798157-A-G		not specified	Likely benign (Oct 01, 2024)
1-203798157-A-T		not specified	Uncertain significance (Feb 06, 2023)
1-203798237-G-A		not specified	Uncertain significance (Mar 11, 2022)
1-203798246-G-C		not specified	Uncertain significance (Apr 06, 2024)
1-203798247-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-203798292-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-203798519-G-C		not specified	Uncertain significance (Dec 02, 2024)
1-203798540-A-C		not specified	Uncertain significance (May 31, 2023)
1-203798540-A-G		not specified	Uncertain significance (Sep 09, 2024)
1-203798546-C-T		not specified	Uncertain significance (Oct 04, 2024)
1-203798579-A-C		not specified	Uncertain significance (Jun 17, 2022)
1-203798607-A-T		not specified	Uncertain significance (Jul 14, 2021)
1-203798675-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-203798697-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-203798702-G-C		not specified	Uncertain significance (Apr 15, 2024)
1-203798705-C-G		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H11A	protein_coding	protein_coding	ENST00000545588	16	58471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000413	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	335	434	0.772	0.0000233	5256
Missense in Polyphen		53	113.32	0.46769		1475
Synonymous	0.636	144	154	0.935	0.00000790	1601
Loss of Function	5.56	3	41.8	0.0718	0.00000240	516

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in nuclear mRNA export; probably mediated by association with the TREX complex. {ECO:0000269|PubMed:22928037}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.474
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h11a

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;RNA export from nucleus;mRNA export from nucleus;poly(A)+ mRNA export from nucleus;mRNA 3'-end processing
• Cellular component: transcription export complex;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA binding;mRNA binding;protein binding;metal ion binding