ZNF43

protein-coding

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

Gene summary

This gene belongs to the C2H2-type zinc finger gene family. The zinc finger proteins are involved in gene regulation and development, and are quite conserved throughout evolution. Like this gene product, a third of the zinc finger proteins containing C2H2 fingers also contain the KRAB domain, which has been found to be involved in protein-protein interactions. [provided by RefSeq, Jul 2008]

Previous symbols:

ZNF39L1

MANE transcript

NM_003423.4

Inheritance

—

ClinVar variants

U:12B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr19:21,804,946-21,852,125

External References & Databases

Ensembl (ENSG00000198521)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF43 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003423.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			9 clinvar	1 clinvar		10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	12	2	0	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003423.4	RefSeq	NP_003414.2	4	MANE Select
ENST00000354959.9	Ensembl	ENSP00000347045.4	4	MANE Select
NM_001256648.2	RefSeq	NP_001243577.1	3	Standard
NM_001256649.2	RefSeq	NP_001243578.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354959
Coding exons: 4
Length: 47176
Individuals with no LoFs: 125636
Homozygous LoFs: 1
Heterozygous LoFs: 109
Defined: 125746
p: 0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.753	445	402	1.11	0.0000182	5374
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.0090	0.0089	notable
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000066	0.000065	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0717

Intolerance Scores

LoFtool: 0.731
RVIS EVS: 0.38
RVIS percentile EVS: 75.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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