HBP1

HMG-box transcription factor 1

Basic information

Region (hg38): 7:107168960-107202522

Links

ENSG00000105856 ∙ NCBI:26959 ∙ OMIM:616714 ∙ HGNC:23200 ∙ Uniprot:O60381 ∙ 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 HBP1 gene.

• Inborn genetic diseases (16 variants)
• COG5-congenital disorder of glycosylation (11 variants)
• not provided (2 variants)
• Congenital disorder of glycosylation (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBP1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	2	1	13
Total	0	0	26	2	1

Variants in HBP1

This is a list of pathogenic ClinVar variants found in the HBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-107169848-G-C			Benign (Feb 18, 2020)
7-107179904-A-G		not specified	Uncertain significance (Jul 16, 2021)
7-107179933-G-A		not specified	Uncertain significance (Nov 03, 2022)
7-107180042-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-107180057-A-G		not specified	Uncertain significance (Aug 12, 2021)
7-107182579-A-G		not specified	Uncertain significance (Mar 08, 2024)
7-107185859-C-T		not specified	Uncertain significance (Jan 17, 2023)
7-107185925-C-T		not specified	Uncertain significance (Jun 11, 2021)
7-107186631-A-G		not specified	Uncertain significance (Jun 06, 2023)
7-107186644-G-A		not specified	Uncertain significance (Jan 09, 2024)
7-107189306-T-A		not specified	Uncertain significance (Nov 17, 2022)
7-107190239-T-C		not specified	Uncertain significance (Nov 21, 2023)
7-107190259-C-G		not specified	Uncertain significance (Jan 23, 2024)
7-107190271-G-A		not specified	Uncertain significance (Jan 10, 2022)
7-107195896-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-107195911-C-T		not specified	Uncertain significance (Nov 20, 2023)
7-107195933-A-C		not specified	Uncertain significance (Jun 22, 2021)
7-107196033-T-G		not specified	Uncertain significance (Jan 17, 2023)
7-107196037-G-A		not specified	Uncertain significance (Jun 09, 2022)
7-107196057-C-T		not specified	Uncertain significance (Dec 12, 2022)
7-107200293-A-G		not specified	Uncertain significance (Mar 08, 2024)
7-107201418-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-107201425-A-T		not specified	Uncertain significance (Jan 30, 2024)
7-107201426-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-107201774-C-T		COG5-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HBP1	protein_coding	protein_coding	ENST00000222574	10	33569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00424	0.995	125634	1	107	125742	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	197	273	0.721	0.0000133	3390
Missense in Polyphen		39	110.42	0.35319		1346
Synonymous	-0.986	106	93.8	1.13	0.00000452	928
Loss of Function	3.17	9	26.6	0.338	0.00000123	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000622	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00547	0.00523
Finnish	0.00	0.00
European (Non-Finnish)	0.0000978	0.0000879
Middle Eastern	0.00547	0.00523
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that binds to the promoter region of target genes. Plays a role in the regulation of the cell cycle and of the Wnt pathway. Binds preferentially to the sequence 5'-TTCATTCATTCA-3'. Binding to the H1F0 promoter is enhanced by interaction with RB1. Disrupts the interaction between DNA and TCF4. {ECO:0000269|PubMed:10562551, ECO:0000269|PubMed:10958660, ECO:0000269|PubMed:11500377}.
• Pathway: Validated transcriptional targets of TAp63 isoforms;C-MYC pathway;Regulation of nuclear beta catenin signaling and target gene transcription;Signaling mediated by p38-alpha and p38-beta;Validated transcriptional targets of deltaNp63 isoforms;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.218
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.557
• hipred: Y
• hipred_score: 0.843
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hbp1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell cycle arrest;Wnt signaling pathway
• Cellular component: nucleoplasm;nuclear speck
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;RNA binding;protein binding