HOXB8

homeobox B8, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48611376-48615292

Previous symbols: [ "HOX2", "HOX2D" ]

Links

ENSG00000120068 ∙ NCBI:3218 ∙ OMIM:142963 ∙ HGNC:5119 ∙ Uniprot:P17481 ∙ 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 HOXB8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB8 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			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in HOXB8

This is a list of pathogenic ClinVar variants found in the HOXB8 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48613230-C-T		not specified	Uncertain significance (Aug 21, 2023)
17-48613251-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-48613261-G-C			Benign (Jul 04, 2018)
17-48613284-T-G		not specified	Uncertain significance (Jan 08, 2024)
17-48613306-A-T		not specified	Uncertain significance (Jan 24, 2024)
17-48613497-C-G		not specified	Uncertain significance (Dec 09, 2023)
17-48613506-G-A		not specified	Uncertain significance (Aug 04, 2021)
17-48614289-C-T		not specified	Uncertain significance (Dec 17, 2023)
17-48614355-C-T		not specified	Uncertain significance (Dec 13, 2021)
17-48614461-G-T		not specified	Uncertain significance (Jan 30, 2024)
17-48614482-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-48614540-C-G		not specified	Uncertain significance (Jun 21, 2023)
17-48614555-G-T		not specified	Uncertain significance (Jan 02, 2024)
17-48614619-G-C		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB8	protein_coding	protein_coding	ENST00000239144	2	3740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.152	125736	0	7	125743	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	100	139	0.721	0.00000621	1567
Missense in Polyphen		35	52.95	0.661		652
Synonymous	-0.833	72	63.5	1.13	0.00000308	479
Loss of Function	2.73	1	10.6	0.0947	4.64e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000233	0.000231
European (Non-Finnish)	0.00	0.00
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.

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.397
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.707
• hipred: Y
• hipred_score: 0.837

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb8
• 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system 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); 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); craniofacial phenotype

Zebrafish Information Network

• Gene name: hoxb8a
• Affected structure: posterior lateral line primordium
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;grooming behavior;adult locomotory behavior;anterior/posterior pattern specification;sensory perception of pain;dorsal spinal cord development;negative regulation of myeloid cell differentiation;embryonic skeletal system morphogenesis
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding