HOXB7

homeobox B7, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 17:48607232-48633572

Previous symbols: [ "HOX2", "HOX2C" ]

Links

ENSG00000260027 ∙ NCBI:3217 ∙ OMIM:142962 ∙ HGNC:5118 ∙ Uniprot:P09629 ∙ 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 HOXB7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXB7 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				2		2
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in HOXB7

This is a list of pathogenic ClinVar variants found in the HOXB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48607851-C-G		not specified	Uncertain significance (May 14, 2024)
17-48607865-C-T		not specified	Uncertain significance (Nov 07, 2023)
17-48607900-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-48607984-G-A		not specified	Uncertain significance (Jan 23, 2023)
17-48608021-T-C		not specified	Uncertain significance (Dec 03, 2021)
17-48608042-G-C		not specified	Uncertain significance (Oct 22, 2024)
17-48610524-C-T		not specified	Uncertain significance (Mar 08, 2025)
17-48610554-C-T		not specified	Uncertain significance (Sep 26, 2024)
17-48610563-G-T		not specified	Uncertain significance (Oct 04, 2024)
17-48610570-C-A		not specified	Uncertain significance (Oct 12, 2024)
17-48610572-G-A		not specified	Uncertain significance (Sep 01, 2024)
17-48610578-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-48610581-T-C		not specified	Uncertain significance (Mar 04, 2024)
17-48610588-T-C		not specified	Uncertain significance (Jan 07, 2022)
17-48610633-G-A		not specified	Uncertain significance (Dec 20, 2021)
17-48610648-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-48610650-G-C		not specified	Uncertain significance (Mar 20, 2024)
17-48610686-T-C			Likely benign (May 01, 2023)
17-48610702-C-T		not specified	Uncertain significance (Mar 01, 2024)
17-48610715-C-G		not specified	Uncertain significance (Apr 20, 2023)
17-48610739-G-A			Likely benign (May 01, 2023)
17-48610762-C-A		not specified	Uncertain significance (Jun 30, 2024)
17-48610764-G-A		not specified	Uncertain significance (Mar 10, 2025)
17-48610775-G-C			Likely benign (May 01, 2023)
17-48610821-G-A		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOXB7	protein_coding	protein_coding	ENST00000239165	2	26341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000284	0.576	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.236	114	121	0.940	0.00000699	1384
Missense in Polyphen		42	42.782	0.98172		472
Synonymous	-0.324	55	52.0	1.06	0.00000289	427
Loss of Function	0.551	6	7.64	0.785	3.98e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000315	0.0000315
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000375	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000669	0.0000653
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.

Recessive Scores

• pRec: 0.192

Haploinsufficiency Scores

• pHI: 0.717
• hipred: Y
• hipred_score: 0.678

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hoxb7
• Phenotype: endocrine/exocrine gland phenotype; hematopoietic system phenotype; immune system phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: hoxb7a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: shortened

Gene ontology

• Biological process: regulation of transcription, DNA-templated;multicellular organism development;anterior/posterior pattern specification;myeloid cell differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;positive regulation of branching involved in ureteric bud morphogenesis
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear body
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer 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;protein binding