HOXB5

homeobox B5, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48591257-48593779

Previous symbols: [ "HOX2", "HOX2A" ]

Links

ENSG00000120075 ∙ NCBI:3215 ∙ OMIM:142960 ∙ HGNC:5116 ∙ Uniprot:P09067 ∙ 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 HOXB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB5 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in HOXB5

This is a list of pathogenic ClinVar variants found in the HOXB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48592258-T-A		not specified	Uncertain significance (Apr 24, 2024)
17-48592265-C-T		not specified	Uncertain significance (Aug 28, 2024)
17-48592318-G-C		not specified	Uncertain significance (Aug 10, 2024)
17-48593127-T-G		not specified	Uncertain significance (Feb 17, 2024)
17-48593259-G-C		not specified	Uncertain significance (Jan 03, 2024)
17-48593277-C-T		not specified	Uncertain significance (Sep 09, 2024)
17-48593285-A-G		not specified	Uncertain significance (Dec 02, 2024)
17-48593306-G-T		not specified	Uncertain significance (May 15, 2024)
17-48593328-C-A		not specified	Uncertain significance (Sep 21, 2021)
17-48593342-G-A		not specified	Uncertain significance (Mar 25, 2024)
17-48593441-T-C		not specified	Uncertain significance (Mar 29, 2022)
17-48593470-C-G		not specified	Uncertain significance (Jan 24, 2024)
17-48593475-C-T		not specified	Uncertain significance (Apr 04, 2024)
17-48593527-C-T		not specified	Uncertain significance (Nov 27, 2024)
17-48593589-C-A		not specified	Uncertain significance (Apr 08, 2024)
17-48593604-C-T		not specified	Uncertain significance (Sep 03, 2024)
17-48593623-C-A		not specified	Uncertain significance (Jul 09, 2024)
17-48593649-G-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB5	protein_coding	protein_coding	ENST00000239151	2	2705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.696	0.301	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.108	156	160	0.976	0.00000749	1762
Missense in Polyphen		45	57.283	0.78557		648
Synonymous	0.343	67	70.7	0.948	0.00000340	551
Loss of Function	2.33	1	8.20	0.122	3.50e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000917	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.000167	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: 0.167

Intolerance Scores

• loftool: 0.206
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.981
• hipred: Y
• hipred_score: 0.697
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb5
• 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)

Zebrafish Information Network

• Gene name: hoxb5b
• Affected structure: presumptive atrium primitive heart tube
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: anatomical structure morphogenesis;anterior/posterior pattern specification;endothelial cell differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis
• Cellular component: fibrillar center;nucleus;cytosol
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding