HBP1

HMG-box transcription factor 1

Basic information

Region (hg38): 7:107168961-107202522

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.

not_specified (48 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. These statistics are base on transcript: NM_000012257.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	0	0

Loading clinvar variants...

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
Phenotype

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