ZCCHC7

zinc finger CCHC-type containing 7, the group of Zinc fingers CCHC-type

Basic information

Region (hg38): 9:37120574-37358149

Links

ENSG00000147905 ∙ NCBI:84186 ∙ ∙ HGNC:26209 ∙ Uniprot:Q8N3Z6 ∙ 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 ZCCHC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC7 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			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	3	0

Variants in ZCCHC7

This is a list of pathogenic ClinVar variants found in the ZCCHC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-37126439-A-G		not specified	Uncertain significance (Sep 20, 2023)
9-37126493-A-G		not specified	Uncertain significance (May 01, 2024)
9-37126526-C-T		not specified	Uncertain significance (Sep 14, 2022)
9-37126558-G-A		not specified	Likely benign (Nov 15, 2021)
9-37126568-A-T		not specified	Uncertain significance (Mar 15, 2024)
9-37126636-A-G		not specified	Uncertain significance (Oct 08, 2024)
9-37126660-G-C		not specified	Uncertain significance (Feb 27, 2024)
9-37126741-A-G		not specified	Uncertain significance (Nov 29, 2023)
9-37126844-A-G		not specified	Uncertain significance (May 22, 2023)
9-37126853-A-G		not specified	Uncertain significance (Jul 14, 2023)
9-37126931-C-T		not specified	Uncertain significance (Feb 09, 2023)
9-37304198-C-G		not specified	Likely benign (Nov 10, 2022)
9-37304236-T-C		not specified	Uncertain significance (Oct 10, 2023)
9-37304239-T-G			Likely benign (May 01, 2023)
9-37305573-G-T		not specified	Uncertain significance (Jan 16, 2024)
9-37305593-C-T		not specified	Uncertain significance (Dec 02, 2022)
9-37305599-C-T		not specified	Uncertain significance (Nov 28, 2024)
9-37349382-C-T		not specified	Uncertain significance (Aug 28, 2024)
9-37349421-A-G		not specified	Uncertain significance (Aug 26, 2022)
9-37349429-G-A		not specified	Uncertain significance (Aug 30, 2021)
9-37349439-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-37349443-T-G		not specified	Uncertain significance (May 30, 2023)
9-37349451-A-C		not specified	Uncertain significance (Jun 09, 2022)
9-37356852-G-A		not specified	Uncertain significance (Nov 14, 2024)
9-37356906-C-G		not specified	Uncertain significance (Nov 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC7	protein_coding	protein_coding	ENST00000336755	8	237611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.86e-9	0.937	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	273	290	0.942	0.0000150	3606
Missense in Polyphen		100	98.239	1.0179		1229
Synonymous	0.787	92	102	0.901	0.00000523	941
Loss of Function	1.93	18	29.3	0.614	0.00000176	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000816	0.000815
Ashkenazi Jewish	0.00	0.00
East Asian	0.000550	0.000544
Finnish	0.000694	0.000693
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000550	0.000544
South Asian	0.000172	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Pathway: RNA degradation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.928
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.146
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc7

Zebrafish Information Network

• Gene name: zcchc7
• Affected structure: pharyngeal arch 3-7
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Cellular component: nucleolus;cytosol
• Molecular function: RNA binding;protein binding;zinc ion binding