HOXB4

homeobox B4, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48575507-48578350

Previous symbols: [ "HOX2", "HOX2F" ]

Links

ENSG00000182742

∙ NCBI:3214 ∙ OMIM:142965 ∙ HGNC:5115 ∙ Uniprot:P17483 ∙ 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 HOXB4 gene.

not_specified (37 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024015.5. 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			37 clinvar			37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB4	protein_coding	protein_coding	ENST00000332503	2	4599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0598	0.875	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.550	106	123	0.861	0.00000557	1591
Missense in Polyphen		32	52.321	0.61161		598
Synonymous	0.161	52	53.5	0.972	0.00000242	534
Loss of Function	1.55	3	7.60	0.395	3.23e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	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.;
Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Recessive Scores

pRec: 0.252

Intolerance Scores

loftool: 0.392
rvis_EVS: 0.3
rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

pHI: 0.358
hipred: N
hipred_score: 0.272
ghis: 0.437

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hoxb4
Phenotype: immune system phenotype; skeleton phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal 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); muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;skeletal system development;morphogenesis of an epithelial sheet;cell population proliferation;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;somatic stem cell division;spleen development;bone marrow development;embryonic skeletal system morphogenesis;definitive hemopoiesis;hematopoietic stem cell differentiation;positive regulation of stem cell differentiation
Cellular component: nucleus;centrosome
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;activating transcription factor binding