HOXB13

homeobox B13, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48724762-48728750

Links

ENSG00000159184 ∙ NCBI:10481 ∙ OMIM:604607 ∙ HGNC:5112 ∙ Uniprot:Q92826 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• prostate cancer, hereditary, 9 (Strong), mode of inheritance: AD
• prostate cancer (Definitive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HOXB13 gene.

• not provided (790 variants)
• Hereditary cancer-predisposing syndrome (559 variants)
• Prostate cancer, hereditary, 1 (99 variants)
• not specified (18 variants)
• Prostate cancer, hereditary, 9 (15 variants)
• HOXB13-related condition (8 variants)
• Gastric cancer (3 variants)
• Inborn genetic diseases (2 variants)
• Carcinoma of pancreas (1 variants)
• Breast and/or ovarian cancer (1 variants)
• HOXB13-Related Cancer Predisposition (1 variants)
• Familial prostate carcinoma (1 variants)
• Prostate cancer susceptibility (1 variants)
• HOXB13-related disorders (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB13 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			4	237	3	244
missense			564	1		565
nonsense			28			28
start loss			4			4
frameshift			49			49
inframe indel			9			9
splice donor/acceptor (+/-2bp)			3			3
splice region			7	3		10
non coding			3	18	5	26
Total	0	0	664	256	8

Variants in HOXB13

This is a list of pathogenic ClinVar variants found in the HOXB13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48726629-A-AG		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726634-G-GC		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726636-TC-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726637-C-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726638-C-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726638-C-CG		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726640-GA-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726640-G-GC		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726642-G-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726643-GA-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726644-A-C		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726644-A-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726646-CA-C		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726648-G-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726650-C-A		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726650-C-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726651-CA-C		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726652-A-C		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726653-G-A		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726653-G-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726654-C-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726655-A-C		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726658-C-G		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726658-C-T		Prostate cancer, hereditary, 1	Uncertain significance (-)
17-48726658-CA-C		Prostate cancer, hereditary, 1	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB13	protein_coding	protein_coding	ENST00000290295	2	4416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.69e-8	0.106	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00415	166	166	1.00	0.00000840	1803
Missense in Polyphen		55	58.371	0.94224		699
Synonymous	-0.588	79	72.6	1.09	0.00000391	614
Loss of Function	-0.208	11	10.3	1.07	4.95e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
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. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000269|PubMed:28473536}.
• Disease: DISEASE: Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:22236224, ECO:0000269|PubMed:22714738, ECO:0000269|PubMed:23064873, ECO:0000269|PubMed:23292082, ECO:0000269|PubMed:25629170, ECO:0000269|PubMed:27424772}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.364
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.490
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb13
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; reproductive system phenotype; limbs/digits/tail 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; cellular phenotype; endocrine/exocrine gland 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;epidermis development;response to wounding;response to testosterone;regulation of growth;prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis;epithelial cell maturation involved in prostate gland development
• Cellular component: nucleoplasm;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;methyl-CpG binding;sequence-specific DNA binding