HOXB2

homeobox B2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48540893-48545109

Previous symbols: [ "HOX2", "HOX2H" ]

Links

ENSG00000173917 ∙ NCBI:3212 ∙ OMIM:142967 ∙ HGNC:5113 ∙ Uniprot:P14652 ∙ 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 HOXB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB2 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in HOXB2

This is a list of pathogenic ClinVar variants found in the HOXB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48543130-A-G		not specified	Uncertain significance (Dec 16, 2023)
17-48543213-A-T		not specified	Uncertain significance (Oct 03, 2022)
17-48543214-A-T		not specified	Uncertain significance (Oct 03, 2022)
17-48543231-A-G		not specified	Uncertain significance (Mar 07, 2023)
17-48543241-C-A		not specified	Uncertain significance (Jan 18, 2023)
17-48543262-C-G		not specified	Uncertain significance (Aug 02, 2021)
17-48543263-T-G		not specified	Uncertain significance (Nov 09, 2022)
17-48543274-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-48543292-C-A		not specified	Uncertain significance (Apr 25, 2022)
17-48543322-A-C		not specified	Uncertain significance (Nov 15, 2021)
17-48543342-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-48543346-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-48543361-G-T		not specified	Uncertain significance (Jan 26, 2023)
17-48543445-G-C		not specified	Uncertain significance (Sep 25, 2023)
17-48543457-G-C		not specified	Uncertain significance (Apr 22, 2022)
17-48543490-C-G		not specified	Uncertain significance (Aug 01, 2022)
17-48543525-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-48543526-G-C		not specified	Uncertain significance (Aug 14, 2023)
17-48543540-C-G		not specified	Uncertain significance (Jul 06, 2021)
17-48544547-G-A		not specified	Uncertain significance (Sep 23, 2023)
17-48544577-G-A		not specified	Uncertain significance (May 04, 2022)
17-48544637-G-A		not specified	Uncertain significance (Apr 23, 2024)
17-48544649-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-48544691-T-G		not specified	Uncertain significance (Oct 26, 2022)
17-48544731-A-G		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB2	protein_coding	protein_coding	ENST00000330070	2	5186

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000146	0.674	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.57	270	206	1.31	0.00000940	2249
Missense in Polyphen		84	74.181	1.1324		878
Synonymous	-0.686	107	98.4	1.09	0.00000472	793
Loss of Function	0.844	7	9.86	0.710	4.20e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000240
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000326
Finnish	0.000201	0.000185
European (Non-Finnish)	0.000230	0.000220
Middle Eastern	0.000335	0.000326
South Asian	0.000599	0.000588
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. {ECO:0000269|PubMed:10595394}.
• Pathway: Activation of anterior HOX genes in hindbrain development during early embryogenesis (Consensus)

Intolerance Scores

• loftool: 0.292
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.382
• hipred: N
• hipred_score: 0.178
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb2
• Phenotype: normal 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); embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; hearing/vestibular/ear 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); muscle phenotype; vision/eye phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: morphogenesis of an epithelial sheet;multicellular organism development;blood circulation;anterior/posterior pattern specification;dorsal/ventral pattern formation;rhombomere 3 development;rhombomere 4 development;facial nerve structural organization;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;neural nucleus development
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear speck
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding