ZNF830

zinc finger protein 830, the group of Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): 17:34961539-34963777

Previous symbols: [ "CCDC16" ]

Links

ENSG00000198783 ∙ NCBI:91603 ∙ ∙ HGNC:28291 ∙ Uniprot:Q96NB3 ∙ 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 ZNF830 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF830 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						0
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in ZNF830

This is a list of pathogenic ClinVar variants found in the ZNF830 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-34961570-G-T		not specified	Uncertain significance (May 26, 2024)
17-34961595-C-T		not specified	Uncertain significance (Mar 19, 2024)
17-34961621-G-A		not specified	Uncertain significance (Jan 10, 2023)
17-34961694-C-T		not specified	Uncertain significance (Jul 19, 2022)
17-34961717-C-G		not specified	Uncertain significance (Nov 18, 2022)
17-34961744-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-34961751-G-A		not specified	Uncertain significance (Nov 21, 2023)
17-34961766-A-C		not specified	Uncertain significance (Sep 17, 2021)
17-34961805-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-34961867-G-A		not specified	Uncertain significance (Aug 19, 2023)
17-34961883-C-T		not specified	Uncertain significance (Sep 25, 2023)
17-34961908-G-C		not specified	Uncertain significance (Apr 18, 2023)
17-34961946-C-G		not specified	Uncertain significance (Mar 11, 2024)
17-34962090-G-C		not specified	Uncertain significance (Oct 04, 2022)
17-34962099-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-34962108-G-C		not specified	Uncertain significance (Apr 18, 2024)
17-34962135-A-G		not specified	Uncertain significance (Aug 15, 2023)
17-34962144-C-T		not specified	Uncertain significance (Sep 14, 2023)
17-34962163-G-C		not specified	Uncertain significance (Nov 21, 2022)
17-34962185-A-G		not specified	Likely benign (Feb 16, 2023)
17-34962236-G-C		not specified	Uncertain significance (Jan 31, 2023)
17-34962251-G-A		not specified	Uncertain significance (Nov 30, 2022)
17-34962264-A-C		not specified	Uncertain significance (Jun 02, 2024)
17-34962294-C-G		not specified	Uncertain significance (Dec 03, 2021)
17-34962377-G-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF830	protein_coding	protein_coding	ENST00000361952	1	1657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0596	0.925	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.403	190	206	0.921	0.00000923	2437
Missense in Polyphen		59	84.153	0.7011		1043
Synonymous	-1.25	99	84.4	1.17	0.00000406	726
Loss of Function	2.11	4	11.9	0.337	5.16e-7	154

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in pre-mRNA splicing as component of the spliceosome (PubMed:25599396). Acts as an important regulator of the cell cycle that participates in the maintenance of genome integrity. During cell cycle progression in embryonic fibroblast, prevents replication fork collapse, double-strand break formation and cell cycle checkpoint activation. Controls mitotic cell cycle progression and cell survival in rapidly proliferating intestinal epithelium and embryonic stem cells. During the embryo preimplantation, controls different aspects of M phase. During early oocyte growth, plays a role in oocyte survival by preventing chromosomal breaks formation, activation of TP63 and reduction of transcription (By similarity). {ECO:0000250|UniProtKB:Q8R1N0, ECO:0000305|PubMed:25599396}.
• Pathway: DNA Repair;Formation of TC-NER Pre-Incision Complex;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• loftool: 0.385
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.739
• ghis: 0.508

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00545

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp830
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: mitotic cell cycle;ovarian follicle development;preantral ovarian follicle growth;blastocyst growth;transcription-coupled nucleotide-excision repair;mRNA processing;RNA splicing;nuclear DNA replication;mitotic DNA replication checkpoint;negative regulation of apoptotic process;mitotic DNA damage checkpoint;replication fork protection;chromosome organization;cell division;intestinal epithelial structure maintenance
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;chromosome;nuclear speck
• Molecular function: nucleic acid binding;protein binding;zinc ion binding