GeneBe

HP1BP3

heterochromatin protein 1 binding protein 3

Basic information

Region (hg38): 1:20740266-20787323

Links

ENSG00000127483 ∙ NCBI:50809 ∙ OMIM:616072 ∙ HGNC:24973 ∙ Uniprot:Q5SSJ5 ∙ 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 HP1BP3 gene.

  • not_specified (42 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HP1BP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001372052.1. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
40
clinvar
2
clinvar
 42
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 40 2 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HP1BP3protein_codingprotein_codingENST00000312239 1244663
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9840.0158125738091257470.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.211862930.6360.00001493587
Missense in Polyphen51116.540.437611462
Synonymous-1.041251111.130.000006171075
Loss of Function4.16325.80.1160.00000115367

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006190.0000615
Ashkenazi Jewish0.00009920.0000992
East Asian0.00005440.0000544
Finnish0.00009280.0000924
European (Non-Finnish)0.00003530.0000352
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of heterochromatin that maintains heterochromatin integrity during G1/S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity (PubMed:24830416). Mediates chromatin condensation during hypoxia, leading to increased tumor cell viability, radio-resistance, chemo-resistance and self- renewal(PubMed:25100860). {ECO:0000269|PubMed:24830416, ECO:0000269|PubMed:25100860}.;

Recessive Scores

pRec
0.161

Intolerance Scores

loftool
0.260
rvis_EVS
-0.27
rvis_percentile_EVS
34.6

Haploinsufficiency Scores

pHI
0.520
hipred
Y
hipred_score
0.673
ghis
0.617

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.926

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Hp1bp3
Phenotype
growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
nucleosome assembly;regulation of transcription, DNA-templated;regulation of cell population proliferation;heterochromatin organization;cellular response to hypoxia;regulation of nucleus size
Cellular component
nucleosome;nucleus;chromosome;nuclear speck
Molecular function
DNA binding;protein binding;nucleosome binding