HOXB1

homeobox B1, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48528526-48531011

Previous symbols: [ "HOX2", "HOX2I" ]

Links

ENSG00000120094 ∙ NCBI:3211 ∙ OMIM:142968 ∙ HGNC:5111 ∙ Uniprot:P14653 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• facial paresis, hereditary congenital, 3 (Strong), mode of inheritance: AR
• facial paresis, hereditary congenital, 3 (Moderate), mode of inheritance: AR
• facial paresis, hereditary congenital, 3 (Strong), mode of inheritance: AR
• congenital hereditary facial paralysis-variable hearing loss syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Facial paresis, hereditary congenital, 3	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Neurologic; Ophthalmologic	22770981

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HOXB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB1 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				7	3	10
missense			19	3	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	10	6

Variants in HOXB1

This is a list of pathogenic ClinVar variants found in the HOXB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48529578-G-A		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
17-48529581-GA-TT			Uncertain significance (Jul 31, 2018)
17-48529619-C-G		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
17-48529619-C-T			Likely benign (Apr 07, 2018)
17-48529645-G-A		Inborn genetic diseases	Uncertain significance (Mar 13, 2023)
17-48529659-T-C		not specified • Facial paresis, hereditary congenital, 3	Benign (Aug 10, 2021)
17-48529689-C-T		Facial paresis, hereditary congenital, 3	Uncertain significance (Jun 15, 2018)
17-48529725-T-C		Inborn genetic diseases	Uncertain significance (Apr 20, 2023)
17-48529739-G-A		HOXB1-related disorder	Likely benign (Jun 12, 2019)
17-48529751-C-T			Benign/Likely benign (Nov 01, 2023)
17-48529762-C-T		Inborn genetic diseases	Uncertain significance (May 05, 2022)
17-48529833-C-T		Facial paresis, hereditary congenital, 3	Pathogenic (Mar 06, 2018)
17-48529834-G-A		Facial paresis, hereditary congenital, 3	Pathogenic (Jul 13, 2012)
17-48529846-G-C		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
17-48529875-G-C		Inborn genetic diseases	Likely benign (Jun 12, 2023)
17-48529883-C-T			Likely benign (Dec 31, 2019)
17-48530378-G-T		Inborn genetic diseases	Uncertain significance (May 24, 2023)
17-48530417-T-A		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
17-48530421-C-T		HOXB1-related disorder	Likely benign (Feb 13, 2023)
17-48530443-C-T		HOXB1-related disorder	Likely benign (Dec 30, 2019)
17-48530455-C-T			Benign (Nov 12, 2018)
17-48530457-C-T		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
17-48530523-C-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
17-48530561-C-A		Inborn genetic diseases	Uncertain significance (May 31, 2023)
17-48530596-T-A			Benign (Jun 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB1	protein_coding	protein_coding	ENST00000239174	2	2472

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0818	0.909	125714	0	20	125734	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.860	158	191	0.825	0.0000115	1899
Missense in Polyphen		41	66.22	0.61915		714
Synonymous	0.820	74	83.5	0.886	0.00000552	625
Loss of Function	2.27	4	12.7	0.314	8.11e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.0000981	0.0000980
Other	0.000166	0.000163

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. Acts on the anterior body structures.
• Disease: DISEASE: Facial paresis, hereditary congenital, 3 (HCFP3) [MIM:614744]: A form of facial paresis, a disease characterized by isolated dysfunction of the facial nerve (CN VII). HCFP3 patients are affected by bilateral facial palsy, facial muscle weakness of muscles innervated by CN VII, hearing loss, and strabismus. {ECO:0000269|PubMed:22770981}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Neural Crest Differentiation;Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.120
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.782
• hipred: N
• hipred_score: 0.432
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.489

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; muscle phenotype; vision/eye phenotype; craniofacial 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; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton 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); hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: hoxb1a
• Affected structure: Mauthner neuron
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: regulation of transcription, DNA-templated;multicellular organism development;pattern specification process;anterior/posterior pattern specification;rhombomere 4 development;rhombomere 5 development;facial nerve structural organization;facial nucleus development;positive regulation of transcription by RNA polymerase II;anatomical structure formation involved in morphogenesis;embryonic skeletal system morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;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;protein domain specific binding