HOXB6

homeobox B6, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48595751-48604992

Previous symbols: [ "HOX2", "HOX2B" ]

Links

ENSG00000108511 ∙ NCBI:3216 ∙ OMIM:142961 ∙ HGNC:5117 ∙ Uniprot:P17509 ∙ 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 HOXB6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB6 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					6	6
Total	0	0	25	0	7

Variants in HOXB6

This is a list of pathogenic ClinVar variants found in the HOXB6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48596177-C-T			Benign (Nov 12, 2018)
17-48596256-G-A			Benign (Jun 20, 2021)
17-48596361-T-G			Benign (Nov 12, 2018)
17-48596362-C-T			Benign (Nov 12, 2018)
17-48596428-T-G		not specified	Uncertain significance (Jun 13, 2024)
17-48596446-A-C		not specified	Uncertain significance (Jun 13, 2024)
17-48596478-C-T		not specified	Uncertain significance (Oct 16, 2024)
17-48596496-G-A		not specified	Uncertain significance (Oct 01, 2024)
17-48596498-C-T		not specified	Uncertain significance (Dec 06, 2023)
17-48596514-T-C		not specified	Uncertain significance (Jan 08, 2025)
17-48596639-C-A		not specified	Uncertain significance (Jun 07, 2025)
17-48596652-C-T		not specified	Uncertain significance (Jul 21, 2015)
17-48596658-G-C		not specified	Uncertain significance (Aug 01, 2024)
17-48597731-C-G		Meckel syndrome, type 1	Uncertain significance (Mar 25, 2024)
17-48597746-A-T		not specified	Uncertain significance (Dec 19, 2022)
17-48597749-C-T		not specified	Uncertain significance (Nov 21, 2022)
17-48597753-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-48597765-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-48597790-G-C		not specified	Uncertain significance (Mar 21, 2023)
17-48597814-T-A		not specified	Uncertain significance (Jul 19, 2023)
17-48597819-T-C		not specified	Uncertain significance (Jul 12, 2023)
17-48597836-C-G		not specified	Uncertain significance (Feb 16, 2023)
17-48597839-C-T		HOXB6-related disorder	Likely benign (Jun 21, 2022)
17-48597859-G-A		not specified	Uncertain significance (Apr 12, 2022)
17-48597862-G-T		not specified	Uncertain significance (Mar 22, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB6	protein_coding	protein_coding	ENST00000484302	2	10716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000738	0.777	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.140	120	124	0.965	0.00000598	1413
Missense in Polyphen		21	36.159	0.58076		438
Synonymous	-0.770	64	56.6	1.13	0.00000281	439
Loss of Function	1.03	6	9.40	0.638	4.15e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000303	0.0000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000844	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000366	0.0000327
Other	0.000163	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.

Recessive Scores

• pRec: 0.329

Haploinsufficiency Scores

• pHI: 0.445
• hipred: Y
• hipred_score: 0.745
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb6
• 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); hematopoietic system phenotype

Gene ontology

• Biological process: anterior/posterior pattern specification;erythrocyte homeostasis;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA binding;protein binding