BBX

protein-coding

BBX high mobility group box domain containing

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within bone development. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001142568.3

Inheritance

—

ClinVar variants

U:133B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr3:107,522,936-107,811,339

External References & Databases

Ensembl (ENSG00000114439)

Transcript & Mutation Effects

hg38 • Region Span ~288.4 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 BBX variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 127

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142568.3. 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			2 clinvar	3 clinvar	1 clinvar	6
missense			127 clinvar	1 clinvar	2 clinvar	130
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	133	4	3	140

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 88 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142568.3	RefSeq	NP_001136040.1	15	MANE Select
ENST00000325805.13	Ensembl	ENSP00000319974.8	15	MANE Select
NM_001276286.2	RefSeq	NP_001263215.1	14	Standard
NM_020235.7	RefSeq	NP_064620.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
bone development

Molecular Function

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

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325805
Coding exons: 15
Length: 288389
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125734
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	436	505	0.863	0.0000261	6229
Missense (PolyPhen)		194	238.1	0.8148		2879
Synonymous	0.486	173	181	0.954	0.00000996	1732
Loss of Function	4.90	10	45.8	0.218	0.00000265	585

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor that is necessary for cell cycle progression from G1 to S phase. {ECO:0000269|PubMed:11680820}.;

Recessive Scores

pRec: 0.0903

Intolerance Scores

LoFtool: 0.0750
RVIS EVS: 0.01
RVIS percentile EVS: 54.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.327

Gene Damage Prediction

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