ZNF302

zinc finger protein 302, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:34677639-34686397

Links

ENSG00000089335 ∙ NCBI:55900 ∙ ∙ HGNC:13848 ∙ Uniprot:Q9NR11 ∙ 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 ZNF302 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF302 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			27	2	3	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	27	2	3

Variants in ZNF302

This is a list of pathogenic ClinVar variants found in the ZNF302 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34682804-T-G		not specified	Uncertain significance (Feb 10, 2022)
19-34682867-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-34682874-A-G		not specified	Uncertain significance (Dec 22, 2023)
19-34682884-C-A		not specified	Uncertain significance (Sep 17, 2021)
19-34683163-G-A		not specified	Likely benign (Apr 07, 2022)
19-34683176-A-G		not specified	Uncertain significance (Nov 23, 2022)
19-34683235-A-G		not specified	Uncertain significance (Aug 21, 2023)
19-34684259-A-C		not specified	Uncertain significance (Nov 06, 2023)
19-34684267-G-C		not specified	Uncertain significance (Nov 01, 2022)
19-34684326-G-C		not specified	Uncertain significance (Mar 31, 2024)
19-34684401-G-A			Benign (Dec 31, 2019)
19-34684499-G-T		not specified	Uncertain significance (Jul 06, 2022)
19-34684558-T-C		not specified	Uncertain significance (Dec 03, 2021)
19-34684629-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-34684654-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-34684686-A-G		not specified	Uncertain significance (Apr 20, 2024)
19-34684687-G-A			Benign (Dec 31, 2019)
19-34684689-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-34684731-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-34684741-G-T		not specified	Uncertain significance (Sep 14, 2022)
19-34684771-C-G		not specified	Uncertain significance (Apr 19, 2023)
19-34684843-G-T		not specified	Likely benign (Jun 09, 2022)
19-34684845-T-A		not specified	Uncertain significance (Dec 28, 2022)
19-34684860-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-34684912-A-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF302	protein_coding	protein_coding	ENST00000505242	4	8759

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000194	0.909	125318	5	423	125746	0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.511	232	211	1.10	0.0000103	2665
Missense in Polyphen		83	67.759	1.2249		848
Synonymous	-2.52	100	72.7	1.38	0.00000378	667
Loss of Function	1.53	8	14.2	0.563	6.93e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.0181	0.0175
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000320	0.000316
Middle Eastern	0.0181	0.0175
South Asian	0.00127	0.00124
Other	0.00133	0.00130

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: 0.0884

Intolerance Scores

• loftool: 0.709
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.09

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.174
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

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;protein binding;metal ion binding