ZBTB47

protein-coding

zinc finger and BTB domain containing 47, the group of Zinc fingers C2H2-type|BTB domain containing

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF651

MANE transcript

NM_145166.4

Inheritance

ClinVar variants

P:1U:155B:20

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:42,653,697-42,667,580

External References & Databases

Ensembl (ENSG00000114853)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZBTB47 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 120

not providedTotal: 55

ZBTB47-related conditionTotal: 13

ZBTB47-related disorderTotal: 1

SeizureTotal: 1

Neurodevelopmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145166.4. 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	8 clinvar		9
missense	1 clinvar		143 clinvar	12 clinvar		156
nonsense			4 clinvar			4
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	1	0	155	20	0	176

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145166.4	RefSeq	NP_660149.2	5	MANE Select
ENST00000232974.11	Ensembl	ENSP00000232974.6	5	MANE Select
NM_001410746.1	RefSeq	NP_001397675.1	6	Standard
ENST00000505904.1	Ensembl	ENSP00000420968.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
cellular response to DNA damage stimulus

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: ENST00000232974
Coding exons: 5
Length: 13897
Individuals with no LoFs: 125592
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125599
p: 0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.45	275	415	0.662	0.0000278	4813
Missense (PolyPhen)		42	90.888	0.46211		1020
Synonymous	0.232	175	179	0.978	0.0000133	1450
Loss of Function	4.61	0	24.8	0.00	0.00000127	312

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0919

Intolerance Scores

LoFtool: 0.202
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.749

Gene Damage Prediction

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