ZNF30

zinc finger protein 30, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:34926903-34945170

Links

ENSG00000168661 ∙ NCBI:90075 ∙ ∙ HGNC:13090 ∙ Uniprot:P17039 ∙ 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 ZNF30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF30 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in ZNF30

This is a list of pathogenic ClinVar variants found in the ZNF30 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34931867-G-A		not specified	Uncertain significance (Dec 31, 2023)
19-34931868-G-A			Likely benign (Jan 01, 2023)
19-34931915-T-C		not specified	Uncertain significance (Feb 05, 2024)
19-34931927-G-T		not specified	Uncertain significance (Apr 20, 2024)
19-34931971-C-A		not specified	Uncertain significance (Oct 05, 2023)
19-34933703-A-T		not specified	Uncertain significance (Dec 12, 2023)
19-34933719-C-G		not specified	Uncertain significance (Sep 06, 2022)
19-34943240-G-A		not specified	Uncertain significance (May 18, 2022)
19-34943244-C-A		not specified	Uncertain significance (Oct 03, 2023)
19-34943289-T-C		not specified	Uncertain significance (Sep 29, 2023)
19-34943324-C-T		not specified	Uncertain significance (Nov 03, 2022)
19-34943385-G-T		not specified	Uncertain significance (Mar 19, 2024)
19-34943459-A-T		not specified	Uncertain significance (Oct 29, 2021)
19-34943460-T-G		not specified	Uncertain significance (Oct 29, 2021)
19-34943603-A-G		not specified	Uncertain significance (Sep 13, 2023)
19-34943669-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-34943689-T-C			Likely benign (Apr 01, 2023)
19-34943711-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-34943778-C-T		not specified	Uncertain significance (Mar 21, 2023)
19-34943831-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-34943889-G-T		not specified	Uncertain significance (Apr 25, 2022)
19-34943927-T-C		not specified	Uncertain significance (Aug 10, 2023)
19-34944003-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-34944045-A-G		not specified	Uncertain significance (Feb 15, 2023)
19-34944075-A-C		not specified	Uncertain significance (Mar 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF30	protein_coding	protein_coding	ENST00000439785	4	18268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00233	0.550	125087	0	13	125100	0.0000520

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.265	348	334	1.04	0.0000167	4122
Missense in Polyphen		119	109.14	1.0904		1393
Synonymous	1.10	102	117	0.870	0.00000593	1105
Loss of Function	0.253	4	4.58	0.873	1.94e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000545	0.000541
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• loftool: 0.982
• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.93

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.112
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0795

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding