ZCCHC9

protein-coding

zinc finger CCHC-type containing 9, the group of Zinc fingers CCHC-type|Protein phosphatase 1 regulatory subunits

Gene summary

Enables RNA binding activity. Predicted to be involved in DNA-templated transcription. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001131035.2

Inheritance

—

ClinVar variants

U:26B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr5:81,301,587-81,313,297

External References & Databases

Ensembl (ENSG00000131732)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 ZCCHC9 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 27

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001131035.2. 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			26 clinvar	1 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	1	0	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001131035.2	RefSeq	NP_001124507.1	5	MANE Select
ENST00000407610.8	Ensembl	ENSP00000385047.3	5	MANE Select
NM_001131036.2	RefSeq	NP_001124508.1	5	Standard
NM_032280.3	RefSeq	NP_115656.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of phosphatase activity

Molecular Function

RNA binding
zinc ion binding

Cellular Component

nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254037
Coding exons: 5
Length: 11708
Individuals with no LoFs: 125704
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125747
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.567	131	151	0.870	0.00000778	1790
Missense (PolyPhen)		20	39.101	0.51149		495
Synonymous	1.25	39	50.3	0.776	0.00000269	481
Loss of Function	1.80	7	14.3	0.488	8.38e-7	168

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May down-regulate transcription mediated by NF-kappa-B and the serum response element. {ECO:0000269|PubMed:18721783}.;

Recessive Scores

pRec: 0.0958

Intolerance Scores

LoFtool: 0.936
RVIS EVS: 0.48
RVIS percentile EVS: 79.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.417

Gene Damage Prediction

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