ZNF630

zinc finger protein 630, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:47983356-48071658

Links

ENSG00000221994 ∙ NCBI:57232 ∙ OMIM:300819 ∙ HGNC:28855 ∙ Uniprot:Q2M218 ∙ 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 ZNF630 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF630 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				1		1
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	23	2	0

Variants in ZNF630

This is a list of pathogenic ClinVar variants found in the ZNF630 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48008414-G-A		not specified	Uncertain significance (Apr 13, 2022)
X-48008513-C-G		not specified	Uncertain significance (Feb 01, 2023)
X-48008530-T-G		not specified	Uncertain significance (Apr 15, 2024)
X-48058467-A-G			Likely benign (Nov 01, 2022)
X-48058475-A-G		not specified	Uncertain significance (Apr 29, 2024)
X-48058745-G-A		not specified	Uncertain significance (Oct 27, 2022)
X-48058872-A-T		not specified	Uncertain significance (Mar 25, 2024)
X-48058910-C-T		not specified	Uncertain significance (Jan 04, 2024)
X-48058911-C-G		not specified	Uncertain significance (Apr 27, 2022)
X-48058971-C-G		not specified	Uncertain significance (Jan 17, 2024)
X-48058985-G-T		not specified	Uncertain significance (Nov 30, 2022)
X-48059016-C-T		not specified	Uncertain significance (Jun 02, 2024)
X-48059201-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-48059202-G-A		not specified	Uncertain significance (Apr 06, 2022)
X-48059270-A-G		not specified	Uncertain significance (Nov 18, 2022)
X-48059333-G-A		not specified	Uncertain significance (Dec 27, 2023)
X-48059402-T-C		not specified	Uncertain significance (Jul 06, 2022)
X-48059483-T-A		not specified	Uncertain significance (Dec 09, 2023)
X-48059611-C-G		not specified	Uncertain significance (Aug 14, 2023)
X-48059731-A-G			Likely benign (Nov 01, 2022)
X-48059792-G-A			Likely benign (-)
X-48059945-G-T		not specified	Uncertain significance (Aug 02, 2021)
X-48060168-T-C		not specified	Uncertain significance (Oct 25, 2022)
X-48060482-A-G		not specified	Uncertain significance (May 05, 2022)
X-48060489-A-G		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF630	protein_coding	protein_coding	ENST00000409324	4	88270

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000119	0.846	125214	16	40	125270	0.000224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.145	230	224	1.03	0.0000150	4361
Missense in Polyphen		51	57.248	0.89087		1173
Synonymous	0.722	69	77.1	0.895	0.00000513	1161
Loss of Function	1.31	8	13.1	0.610	8.21e-7	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00144
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000164
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000124
Middle Eastern	0.000217	0.000164
South Asian	0.000160	0.0000982
Other	0.000222	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.862
• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA binding;metal ion binding