HOXB3

protein-coding

homeobox B3, the group of HOXL subclass homeoboxes|MicroRNA protein coding host genes

Gene summary

This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development. Increased expression of this gene is associated with a distinct biologic subset of acute myeloid leukemia (AML). [provided by RefSeq, Jul 2008]

Previous symbols:

HOX2
HOX2G

MANE transcript

NM_001384749.1

Inheritance

—

ClinVar variants

U:78B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr17:48,548,870-48,604,912

External References & Databases

Ensembl (ENSG00000120093)

Transcript & Mutation Effects

hg38 • Region Span ~56.0 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 HOXB3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 118

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384749.1. 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			78 clinvar			78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	1	0	79

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384749.1	RefSeq	NP_001371678.1	2	MANE Select
ENST00000498678.6	Ensembl	ENSP00000420595.1	2	MANE Select
NM_001330322.2	RefSeq	NP_001317251.1	2	Standard
NM_001330323.1	RefSeq	NP_001317252.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Activation of anterior HOX genes in hindbrain development during early embryogenesis

Biological Process

negative regulation of transcription by RNA polymerase II
angiogenesis
hematopoietic progenitor cell differentiation
anterior/posterior pattern specification
rhombomere development

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000470495
Coding exons: 2
Length: 56043
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125737
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.116	270	275	0.980	0.0000167	2747
Missense (PolyPhen)		91	91.916	0.99003		898
Synonymous	-0.160	140	138	1.02	0.0000101	916
Loss of Function	2.88	1	11.6	0.0862	4.96e-7	131

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.;

Intolerance Scores

LoFtool: 0.112
RVIS EVS: -0.23
RVIS percentile EVS: 37.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.873

Gene Damage Prediction

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