HOXB3

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

Basic information

Region (hg38): 17:48548869-48604912

Previous symbols: [ "HOX2", "HOX2G" ]

Links

ENSG00000120093 ∙ NCBI:3213 ∙ OMIM:142966 ∙ HGNC:5114 ∙ Uniprot:P14651 ∙ 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 HOXB3 gene.

• Inborn genetic diseases (41 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB3 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						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			16			16
Total	0	0	41	0	0

Variants in HOXB3

This is a list of pathogenic ClinVar variants found in the HOXB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48550402-G-C		not specified	Uncertain significance (Jan 22, 2024)
17-48550425-T-G		not specified	Uncertain significance (Nov 01, 2022)
17-48550432-G-A		not specified	Uncertain significance (Jul 06, 2022)
17-48550482-T-C		not specified	Uncertain significance (Mar 28, 2023)
17-48550496-A-T		not specified	Uncertain significance (Dec 08, 2021)
17-48550545-A-C		not specified	Uncertain significance (Aug 12, 2021)
17-48550558-A-C		not specified	Uncertain significance (Feb 09, 2022)
17-48550564-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-48550599-G-C		not specified	Uncertain significance (Jul 21, 2021)
17-48550606-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-48550614-C-T		not specified	Uncertain significance (Dec 16, 2023)
17-48550618-C-T		not specified	Uncertain significance (Jun 01, 2022)
17-48550624-C-T		not specified	Uncertain significance (Aug 30, 2022)
17-48550642-C-T		not specified	Uncertain significance (Oct 25, 2023)
17-48550662-G-A		not specified	Uncertain significance (Jun 21, 2021)
17-48550668-T-A			Uncertain significance (Jan 01, 2024)
17-48550736-G-C		not specified	Uncertain significance (May 03, 2023)
17-48550756-G-T		not specified	Uncertain significance (Mar 04, 2024)
17-48550776-C-T		not specified	Uncertain significance (Sep 27, 2021)
17-48550813-C-T		not specified	Uncertain significance (Aug 04, 2023)
17-48550816-T-G		not specified	Uncertain significance (Oct 17, 2023)
17-48550854-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-48550855-G-A		not specified	Uncertain significance (Dec 28, 2023)
17-48550861-C-A		not specified	Uncertain significance (Jun 22, 2021)
17-48551094-T-C		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB3	protein_coding	protein_coding	ENST00000470495	2	56043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.108	125732	0	5	125737	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.116	270	275	0.980	0.0000167	2747
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Intolerance Scores

• loftool: 0.112
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.450
• hipred: Y
• hipred_score: 0.650
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb3
• Phenotype: craniofacial phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;hematopoietic progenitor cell differentiation;anterior/posterior pattern specification;rhombomere development;glossopharyngeal nerve morphogenesis;thyroid gland development;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;regulation of neurogenesis;cartilage development;definitive hemopoiesis;face development
• Cellular component: nucleus
• 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