ZNF213

zinc finger protein 213, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 16:3129777-3142804

Links

ENSG00000085644 ∙ NCBI:7760 ∙ OMIM:608387 ∙ HGNC:13005 ∙ Uniprot:O14771 ∙ 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 ZNF213 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF213 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	2	3
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	2

Variants in ZNF213

This is a list of pathogenic ClinVar variants found in the ZNF213 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3137326-G-A		not specified	Uncertain significance (Jun 06, 2023)
16-3137384-A-G		not specified	Uncertain significance (Jun 06, 2023)
16-3137413-C-T		not specified	Uncertain significance (May 27, 2022)
16-3137426-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-3137430-A-G			Benign (Oct 09, 2017)
16-3137444-A-T		not specified	Uncertain significance (Mar 18, 2024)
16-3137495-G-A		not specified	Uncertain significance (Aug 01, 2022)
16-3137516-G-A		not specified	Likely benign (May 31, 2023)
16-3137596-C-T		not specified	Uncertain significance (Apr 08, 2024)
16-3137597-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-3137599-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-3137623-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-3137675-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-3138422-T-C		not specified	Uncertain significance (May 03, 2023)
16-3138425-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-3138428-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-3138457-C-T		not specified	Uncertain significance (Jun 13, 2023)
16-3138473-C-T		not specified	Uncertain significance (Sep 14, 2022)
16-3138499-C-T		not specified	Uncertain significance (Oct 06, 2023)
16-3138523-G-C		not specified	Uncertain significance (Dec 06, 2023)
16-3138530-A-C		not specified	Uncertain significance (Sep 06, 2022)
16-3138778-C-G		not specified	Uncertain significance (Jun 02, 2023)
16-3138779-C-T			Benign (Oct 09, 2017)
16-3138796-C-G		not specified	Uncertain significance (May 08, 2023)
16-3138811-G-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF213	protein_coding	protein_coding	ENST00000396878	5	13029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.46e-8	0.766	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	266	317	0.840	0.0000230	2938
Missense in Polyphen		47	62.116	0.75665		647
Synonymous	-0.430	146	140	1.05	0.0000104	946
Loss of Function	1.37	14	20.7	0.675	0.00000105	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000280	0.000273
Ashkenazi Jewish	0.00	0.00
East Asian	0.000170	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000893	0.0000879
Middle Eastern	0.000170	0.000163
South Asian	0.000197	0.000196
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: 0.105

Intolerance Scores

• loftool: 0.643
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.399
• hipred: N
• hipred_score: 0.238
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.662

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp213

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