ZNF830

protein-coding

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

Gene summary

Predicted to enable nucleic acid binding activity and zinc ion binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CCDC16

MANE transcript

NM_052857.4

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr17:34,961,540-34,963,777

External References & Databases

Ensembl (ENSG00000198783)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF830 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 57

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052857.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			55 clinvar	2 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	2	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052857.4	RefSeq	NP_443089.3	1	MANE Select
ENST00000361952.5	Ensembl	ENSP00000354518.3	1	MANE Select
ENST00000578339.1	Ensembl	ENSP00000463839.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

mitotic cell cycle
ovarian follicle development
preantral ovarian follicle growth
blastocyst growth
transcription-coupled nucleotide-excision repair

Molecular Function

nucleic acid binding
protein binding
zinc ion binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
chromosome
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361952
Coding exons: 1
Length: 1657
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.403	190	206	0.921	0.00000923	2437
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0928

Intolerance Scores

LoFtool: 0.385
RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00545

Gene Damage Prediction

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