HOXB9

homeobox B9, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48621156-48626358

Previous symbols: [ "HOX2E", "HOX2" ]

Links

ENSG00000170689 ∙ NCBI:3219 ∙ OMIM:142964 ∙ HGNC:5120 ∙ Uniprot:P17482 ∙ 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 HOXB9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB9 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					1	1
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	2

Variants in HOXB9

This is a list of pathogenic ClinVar variants found in the HOXB9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48622979-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-48622990-G-A			Benign (Dec 31, 2019)
17-48623007-G-T		not specified	Uncertain significance (Dec 15, 2022)
17-48623029-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-48623123-G-T		not specified	Uncertain significance (Jun 17, 2024)
17-48625762-G-A		not specified	Uncertain significance (Jan 22, 2025)
17-48625768-C-G		not specified	Uncertain significance (Sep 09, 2024)
17-48625801-C-G		not specified	Uncertain significance (Jun 28, 2022)
17-48625804-C-T			Likely benign (Dec 03, 2018)
17-48625813-G-C		not specified	Uncertain significance (Oct 07, 2024)
17-48625852-T-A		not specified	Uncertain significance (Mar 31, 2023)
17-48625864-A-G		not specified	Uncertain significance (Feb 12, 2024)
17-48625879-G-C		not specified	Uncertain significance (Oct 14, 2023)
17-48625889-C-G		not specified	Uncertain significance (Jan 21, 2025)
17-48625900-C-A		not specified	Uncertain significance (Jan 21, 2025)
17-48625932-T-A		not specified	Uncertain significance (Nov 09, 2023)
17-48625959-C-A		not specified	Uncertain significance (Nov 20, 2023)
17-48626025-A-T		not specified	Uncertain significance (Sep 26, 2022)
17-48626038-A-G			Benign (Dec 24, 2018)
17-48626083-A-C		not specified	Uncertain significance (Jul 09, 2021)
17-48626113-G-C		not specified	Uncertain significance (Sep 26, 2024)
17-48626215-C-G		not specified	Uncertain significance (Aug 02, 2021)
17-48626233-C-T		not specified	Uncertain significance (Dec 12, 2023)
17-48626245-T-C		not specified	Uncertain significance (May 15, 2023)
17-48626259-G-A		not specified	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB9	protein_coding	protein_coding	ENST00000311177	2	5322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.312	0.672	125738	0	2	125740	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	131	141	0.930	0.00000689	1595
Missense in Polyphen		54	57.498	0.93916		655
Synonymous	-0.959	71	61.4	1.16	0.00000313	480
Loss of Function	2.03	2	8.32	0.240	3.54e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000897	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
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: btg family proteins and cell cycle regulation (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.162
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.946
• hipred: Y
• hipred_score: 0.689

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb9
• 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); endocrine/exocrine gland phenotype; skeleton phenotype; hematopoietic system phenotype; limbs/digits/tail phenotype; immune system phenotype

Gene ontology

• Biological process: transcription, DNA-templated;anterior/posterior pattern specification;mammary gland development;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development;cell chemotaxis
• Cellular component: nucleoplasm;mitochondrion;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding