ZNF43

zinc finger protein 43, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:21804946-21852125

Previous symbols: [ "ZNF39L1" ]

Links

ENSG00000198521 ∙ NCBI:7594 ∙ OMIM:603972 ∙ HGNC:13109 ∙ Uniprot:P17038 ∙ 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 ZNF43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF43 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in ZNF43

This is a list of pathogenic ClinVar variants found in the ZNF43 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-21807800-G-A		not specified	Uncertain significance (Oct 13, 2021)
19-21808658-C-A		not specified	Uncertain significance (Jul 06, 2021)
19-21808831-T-G		not specified	Uncertain significance (Sep 17, 2021)
19-21808862-T-C		not specified	Uncertain significance (Aug 23, 2021)
19-21809306-C-T		not specified	Likely benign (Jul 06, 2021)
19-21809491-T-C			Likely benign (Sep 01, 2022)
19-21809538-T-C		not specified	Uncertain significance (Nov 12, 2021)
19-21817899-G-T		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF43	protein_coding	protein_coding	ENST00000354959	4	47176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000505	0.463	125636	1	109	125746	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.753	445	402	1.11	0.0000182	5374
Missense in Polyphen		140	126.66	1.1053		1843
Synonymous	-0.437	143	137	1.05	0.00000611	1378
Loss of Function	0.144	5	5.36	0.933	2.27e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000586	0.0000586
Ashkenazi Jewish	0.00901	0.00887
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.000821	0.000815

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: 0.0717

Intolerance Scores

• loftool: 0.731
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.347
• hipred: N
• hipred_score: 0.148
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp458

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