ZCCHC9

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

Basic information

Region (hg38): 5:81301587-81313297

Links

ENSG00000131732 ∙ NCBI:84240 ∙ ∙ HGNC:25424 ∙ Uniprot:Q8N567 ∙ 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 ZCCHC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC9 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in ZCCHC9

This is a list of pathogenic ClinVar variants found in the ZCCHC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-81304873-G-A		not specified	Likely benign (Apr 18, 2023)
5-81304952-A-C		not specified	Uncertain significance (Nov 10, 2022)
5-81304963-A-G		not specified	Uncertain significance (Sep 29, 2023)
5-81305002-A-G		not specified	Uncertain significance (Jul 06, 2021)
5-81305007-C-A		not specified	Uncertain significance (Apr 26, 2023)
5-81305038-C-G		not specified	Uncertain significance (Jan 03, 2024)
5-81305056-G-T		not specified	Uncertain significance (Oct 02, 2023)
5-81308672-G-C		not specified	Uncertain significance (May 26, 2022)
5-81308703-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-81308961-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-81309022-A-T		not specified	Uncertain significance (Aug 21, 2023)
5-81311216-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-81311234-T-C		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC9	protein_coding	protein_coding	ENST00000254037	5	11708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00111	0.957	125704	0	43	125747	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.567	131	151	0.870	0.00000778	1790
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00144	0.00144
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000143	0.000131
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.229
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc9

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: nucleolus
• Molecular function: RNA binding;zinc ion binding