ZNF215

zinc finger protein 215, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 11:6926404-7001004

Links

ENSG00000149054 ∙ NCBI:7762 ∙ OMIM:605016 ∙ HGNC:13007 ∙ Uniprot:Q9UL58 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Beckwith-Wiedemann syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF215 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF215 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			29	3	3	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	29	5	3

Variants in ZNF215

This is a list of pathogenic ClinVar variants found in the ZNF215 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6932310-C-G		not specified	Uncertain significance (Dec 07, 2023)
11-6932384-G-A			Benign (May 14, 2018)
11-6932454-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-6932466-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-6932485-G-T		not specified	Uncertain significance (Jan 16, 2024)
11-6932486-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-6932567-A-T		not specified	Uncertain significance (Feb 28, 2023)
11-6932570-C-G		not specified	Uncertain significance (Dec 06, 2022)
11-6932582-G-T		not specified	Uncertain significance (Sep 03, 2024)
11-6932598-A-C		not specified	Uncertain significance (Aug 12, 2021)
11-6932604-A-G		not specified	Uncertain significance (Mar 04, 2024)
11-6932628-T-C			Benign (May 14, 2018)
11-6932630-G-A		not specified	Uncertain significance (Dec 03, 2024)
11-6932638-C-T			Likely benign (Jun 01, 2023)
11-6932652-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-6941573-A-G		not specified	Uncertain significance (Oct 03, 2023)
11-6941648-C-T		not specified	Likely benign (Nov 29, 2021)
11-6943125-G-A		not specified	Uncertain significance (Sep 08, 2024)
11-6943138-A-T		not specified	Uncertain significance (Jul 11, 2023)
11-6943173-G-A		not specified	Uncertain significance (Aug 21, 2024)
11-6943551-C-G		not specified	Uncertain significance (Jan 19, 2024)
11-6943639-T-C		not specified	Uncertain significance (Feb 09, 2023)
11-6943642-G-A			Likely benign (Dec 31, 2019)
11-6955747-C-A		not specified	Uncertain significance (Dec 08, 2023)
11-6955753-G-A			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF215	protein_coding	protein_coding	ENST00000278319	5	58229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.19e-16	0.0146	125335	2	404	125741	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	323	269	1.20	0.0000132	3466
Missense in Polyphen		74	75.289	0.98287		972
Synonymous	-0.254	96	92.9	1.03	0.00000436	909
Loss of Function	0.193	24	25.0	0.958	0.00000160	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000490	0.000489
Finnish	0.00194	0.00190
European (Non-Finnish)	0.00256	0.00254
Middle Eastern	0.000490	0.000489
South Asian	0.000397	0.000392
Other	0.00229	0.00228

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: 0.0725

Intolerance Scores

• loftool: 0.958
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.0357
• hipred: N
• hipred_score: 0.112
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00212

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