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.

not_specified (26 variants)

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. These statistics are base on transcript: NM_000002147.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			26 clinvar			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	0	0

Loading clinvar variants...

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