ZNF343

zinc finger protein 343, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 20:2481817-2524702

Links

ENSG00000088876 ∙ NCBI:79175 ∙ ∙ HGNC:16017 ∙ Uniprot:Q6P1L6 ∙ 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 ZNF343 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF343 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				9		9
missense			27	4		31
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	13	0

Variants in ZNF343

This is a list of pathogenic ClinVar variants found in the ZNF343 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-2483197-A-C		not specified	Uncertain significance (Dec 12, 2023)
20-2483214-C-T		not specified	Uncertain significance (Jun 24, 2022)
20-2483217-A-G		not specified	Uncertain significance (Feb 15, 2023)
20-2483255-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-2483282-C-T		not specified	Likely benign (Sep 29, 2023)
20-2483283-G-A		not specified	Uncertain significance (May 26, 2023)
20-2483284-G-A			Likely benign (Feb 01, 2024)
20-2483289-A-C		not specified	Uncertain significance (Aug 04, 2021)
20-2483314-G-A			Likely benign (Feb 01, 2024)
20-2483329-T-A			Likely benign (Feb 01, 2024)
20-2483335-T-C			Likely benign (Feb 01, 2024)
20-2483340-T-G			Likely benign (Feb 01, 2024)
20-2483344-A-G			Likely benign (Feb 01, 2024)
20-2483350-A-G			Likely benign (Feb 01, 2024)
20-2483372-A-G		not specified	Uncertain significance (Dec 19, 2022)
20-2483449-C-A		not specified	Uncertain significance (Mar 19, 2024)
20-2483468-C-T		not specified	Uncertain significance (Dec 21, 2022)
20-2483534-C-T		not specified	Uncertain significance (Jan 30, 2024)
20-2483536-A-G			Likely benign (Jan 01, 2024)
20-2483537-C-T		not specified	Uncertain significance (Jun 28, 2022)
20-2483559-C-T		not specified	Uncertain significance (May 13, 2024)
20-2483560-A-G			Likely benign (Feb 01, 2024)
20-2483571-G-C		not specified	Uncertain significance (Jun 10, 2024)
20-2483571-G-T		not specified	Uncertain significance (Dec 20, 2023)
20-2483588-G-A			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF343	protein_coding	protein_coding	ENST00000278772	4	42886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00535	0.726	125552	1	178	125731	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.135	308	315	0.979	0.0000157	3915
Missense in Polyphen		61	72.047	0.84668		949
Synonymous	0.181	115	117	0.979	0.00000603	1083
Loss of Function	0.774	4	6.06	0.660	2.56e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000290	0.000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.00	0.00
South Asian	0.00432	0.00429
Other	0.000654	0.000652

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: 0.0771

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

• pHI: 0.0696
• hipred: N
• hipred_score: 0.112
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0172

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;protein binding;metal ion binding