HMBOX1

homeobox containing 1, the group of HNF class homeoboxes

Basic information

Region (hg38): 8:28890394-29064764

Links

ENSG00000147421 ∙ NCBI:79618 ∙ OMIM:618610 ∙ HGNC:26137 ∙ Uniprot:Q6NT76 ∙ 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 HMBOX1 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMBOX1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in HMBOX1

This is a list of pathogenic ClinVar variants found in the HMBOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-28970140-C-T		not specified	Uncertain significance (Sep 28, 2022)
8-28970174-G-A		not specified	Uncertain significance (Mar 16, 2022)
8-28970251-A-G		not specified	Uncertain significance (May 30, 2023)
8-28970422-A-G		not specified	Uncertain significance (Feb 27, 2024)
8-28970426-G-T		not specified	Uncertain significance (Aug 08, 2022)
8-29018907-T-C		not specified	Uncertain significance (Feb 05, 2024)
8-29045423-A-G		not specified	Uncertain significance (Oct 04, 2022)
8-29051062-A-T		not specified	Uncertain significance (Oct 26, 2022)
8-29051091-C-G		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMBOX1	protein_coding	protein_coding	ENST00000397358	9	174371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00195	125733	0	4	125737	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	129	235	0.548	0.0000123	2766
Missense in Polyphen		40	96.865	0.41294		1080
Synonymous	1.58	67	85.5	0.783	0.00000448	789
Loss of Function	4.46	2	27.0	0.0739	0.00000183	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds directly to 5'-TTAGGG-3' repeats in telomeric DNA (PubMed:23813958, PubMed:23685356). Associates with the telomerase complex at sites of active telomere processing and positively regulates telomere elongation (PubMed:23685356). Important for TERT binding to chromatin, indicating a role in recruitment of the telomerase complex to telomeres (By similarity). Also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) (PubMed:23813958). Enhances formation of telomere C-circles in ALT cells, suggesting a possible role in telomere recombination (PubMed:23813958). Might also be involved in the DNA damage response at telomeres (PubMed:23813958). {ECO:0000250|UniProtKB:Q8BJA3, ECO:0000269|PubMed:23685356, ECO:0000269|PubMed:23813958}.
• Pathway: miR-222 in Exercise-Induced Cardiac Growth (Consensus)

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• loftool: 0.0527
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.483
• hipred: Y
• hipred_score: 0.713
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmbox1
• Phenotype: cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of telomere maintenance via telomerase;positive regulation of chromatin binding;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;regulation of telomerase activity;positive regulation of telomerase activity
• Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytoplasm;cytosol;Cajal body;nuclear body;PML body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded telomeric DNA binding;protein binding;telomeric DNA binding;identical protein binding;sequence-specific DNA binding;protein-containing complex binding